diff --git a/doc/source/tutorials/hydration_freenrg.rst b/doc/source/tutorials/hydration_freenrg.rst index 5ff767df8..2b9a416d6 100644 --- a/doc/source/tutorials/hydration_freenrg.rst +++ b/doc/source/tutorials/hydration_freenrg.rst @@ -167,6 +167,20 @@ Let's examine the directory for the :math:`{\lambda=0}` window of the free leg: gromacs.err gromacs.mdp gromacs.out.mdp gromacs.tpr gromacs.gro gromacs.out gromacs.top +Similarly, we can also set up the same simulations using AMBER: + +.. code-block:: python + + free_amber = BSS.FreeEnergy.Relative(solvated, protocol, engine="amber", work_dir="freenrg_amber/free") + vac_amber = BSS.FreeEnergy.Relative(merged.toSystem(), protocol, engine="amber", work_dir="freenrg_amber/vacuum") + +Let's examine the directory for the :math:`{\lambda=0}` window of the free leg: + +.. code-block:: bash + + $ ls freenrg_amber/free/lambda_0.0000 + amber.cfg amber.err amber.out amber.prm7 amber_ref.rst7 amber.rst7 + There you go! This tutorial has shown you how BioSimSpace can be used to easily set up everything that is needed for complex alchemical free energy simulations. Please visit the :data:`API documentation ` for further information. diff --git a/python/BioSimSpace/Align/_merge.py b/python/BioSimSpace/Align/_merge.py index 9c2b96309..f4693e83e 100644 --- a/python/BioSimSpace/Align/_merge.py +++ b/python/BioSimSpace/Align/_merge.py @@ -27,6 +27,7 @@ __all__ = ["merge"] from sire.legacy import Base as _SireBase +from sire.legacy import IO as _SireIO from sire.legacy import MM as _SireMM from sire.legacy import Mol as _SireMol from sire.legacy import Units as _SireUnits @@ -1389,3 +1390,86 @@ def _is_on_ring(idx, conn): # If we get this far, then the atom is not adjacent to a ring. return False + + +def _removeDummies(molecule, is_lambda1): + """ + Internal function which removes the dummy atoms from one of the endstates + of a merged molecule. + + Parameters + ---------- + + molecule : BioSimSpace._SireWrappers.Molecule + The molecule. + + is_lambda1 : bool + Whether to use the molecule at lambda = 1. + """ + if not molecule._is_perturbable: + raise _IncompatibleError("'molecule' is not a perturbable molecule") + + # Always use the coordinates at lambda = 0. + coordinates = molecule._sire_object.property("coordinates0") + + # Generate a molecule with all dummies present. + molecule = molecule.copy()._toRegularMolecule( + is_lambda1=is_lambda1, generate_intrascale=True + ) + + # Remove the parameters property, if it exists. + if "parameters" in molecule._sire_object.propertyKeys(): + molecule._sire_object = ( + molecule._sire_object.edit().removeProperty("parameters").commit() + ) + + # Set the coordinates to those at lambda = 0 + molecule._sire_object = ( + molecule._sire_object.edit().setProperty("coordinates", coordinates).commit() + ) + + # Extract all the nondummy indices + nondummy_indices = [ + i + for i, atom in enumerate(molecule.getAtoms()) + if "du" not in atom._sire_object.property("ambertype") + ] + + # Create an AtomSelection. + selection = molecule._sire_object.selection() + + # Unselect all of the atoms. + selection.selectNone() + + # Now add all of the nondummy atoms. + for idx in nondummy_indices: + selection.select(_SireMol.AtomIdx(idx)) + + # Create a partial molecule and extract the atoms. + partial_molecule = ( + _SireMol.PartialMolecule(molecule._sire_object, selection).extract().molecule() + ) + + # Remove the incorrect intrascale property. + partial_molecule = ( + partial_molecule.edit().removeProperty("intrascale").molecule().commit() + ) + + # Recreate a BioSimSpace molecule object. + molecule = _Molecule(partial_molecule) + + # Parse the molecule as a GROMACS topology, which will recover the intrascale + # matrix. + gro_top = _SireIO.GroTop(molecule.toSystem()._sire_object) + + # Convert back to a Sire system. + gro_sys = gro_top.toSystem() + + # Add the intrascale property back into the merged molecule. + edit_mol = molecule._sire_object.edit() + edit_mol = edit_mol.setProperty( + "intrascale", gro_sys[_SireMol.MolIdx(0)].property("intrascale") + ) + molecule = _Molecule(edit_mol.commit()) + + return molecule diff --git a/python/BioSimSpace/Align/_squash.py b/python/BioSimSpace/Align/_squash.py new file mode 100644 index 000000000..fa3d6ad79 --- /dev/null +++ b/python/BioSimSpace/Align/_squash.py @@ -0,0 +1,725 @@ +import itertools as _it +import numpy as _np +import os as _os +import parmed as _pmd +import shutil as _shutil +import tempfile + +from sire.legacy import IO as _SireIO +from sire.legacy import Mol as _SireMol + +from ._merge import _removeDummies +from ..IO import readMolecules as _readMolecules, saveMolecules as _saveMolecules +from .._SireWrappers import Molecule as _Molecule + + +def _squash(system, explicit_dummies=False): + """ + Internal function which converts a merged BioSimSpace system into an + AMBER-compatible format, where all perturbed molecules are represented + sequentially, instead of in a mixed topology, like in GROMACS. In the + current implementation, all perturbed molecules are moved at the end of + the squashed system. For example, if we have an input system, containing + regular molecules (M) and perturbed molecules (P): + + M0 - M1 - P0 - M2 - P1 - M3 + + This function will return the following squashed system: + + M0 - M1 - M2 - M3 - P0_A - PO_B - P1_A - P1_B + + Where A and B denote the dummyless lambda=0 and lambda=1 states. In + addition, we also return a mapping between the old unperturbed molecule + indices and the new ones. This mapping can be used during coordinate update. + Updating the coordinates of the perturbed molecules, however, has to be + done manually through the Python layer. + + Parameters + ---------- + + system : BioSimSpace._SireWrappers.System + The system. + + explicit_dummies : bool + Whether to keep the dummy atoms explicit at the endstates or remove them. + + Returns + ------- + + system : BioSimSpace._SireWrappers.System + The output squashed system. + + mapping : dict(sire.legacy.Mol.MolIdx, sire.legacy.Mol.MolIdx) + The corresponding molecule-to-molecule mapping. Only the non-perturbable + molecules are contained in this mapping as the perturbable ones do not + have a one-to-one mapping and cannot be expressed as a dictionary. + """ + # Create a copy of the original system. + new_system = system.copy() + + # Get the perturbable molecules and their corresponding indices. + pertmol_idxs = [ + i + for i, molecule in enumerate(system.getMolecules()) + if molecule.isPerturbable() + ] + pert_mols = system.getPerturbableMolecules() + + # Remove the perturbable molecules from the system. + new_system.removeMolecules(pert_mols) + + # Add them back at the end of the system. This is generally faster than + # keeping their order the same. + new_indices = list(range(system.nMolecules())) + for pertmol_idx, pert_mol in zip(pertmol_idxs, pert_mols): + new_indices.remove(pertmol_idx) + new_system += _squash_molecule(pert_mol, explicit_dummies=explicit_dummies) + + # Create the old molecule index to new molecule index mapping. + mapping = { + _SireMol.MolIdx(idx): _SireMol.MolIdx(i) for i, idx in enumerate(new_indices) + } + + return new_system, mapping + + +def _squash_molecule(molecule, explicit_dummies=False): + """ + This internal function converts a perturbed molecule to a system that is + recognisable to the AMBER alchemical code. If the molecule contains a single + residue, then the squashed system is just the two separate pure endstate + molecules in order. If the molecule contains regular (R) and perturbable (P) + resides of the form: + + R0 - R1 - P0 - R2 - P1 - R3 + + Then a system containing a single molecule will be returned, which is generated + by ParmEd's tiMerge as follows: + + R0 - R1 - P0_A - R2 - P1_A - R3 - P0_B - P1_B + + Where A and B denote the dummyless lambda=0 and lambda=1 states. + + Parameters + ---------- + + molecule : BioSimSpace._SireWrappers.Molecule + The input molecule. + + explicit_dummies : bool + Whether to keep the dummy atoms explicit at the endstates or remove them. + + Returns + ------- + + system : BioSimSpace._SireWrappers.System + The output squashed system. + """ + if not molecule.isPerturbable(): + return molecule + + if explicit_dummies: + # Get the common core atoms + atom_mapping0_common = _squashed_atom_mapping( + molecule, + is_lambda1=False, + explicit_dummies=explicit_dummies, + environment=False, + dummies=False, + ) + atom_mapping1_common = _squashed_atom_mapping( + molecule, + is_lambda1=True, + explicit_dummies=explicit_dummies, + environment=False, + dummies=False, + ) + if set(atom_mapping0_common) != set(atom_mapping1_common): + raise RuntimeError("The MCS atoms don't match between the two endstates") + common_atoms = set(atom_mapping0_common) + + # We make sure we use the same coordinates for the common core at both endstates. + c = molecule.copy()._sire_object.cursor() + for i, atom in enumerate(c.atoms()): + if i in common_atoms: + atom["coordinates1"] = atom["coordinates0"] + molecule = _Molecule(c.commit()) + + # Generate a "system" from the molecule at lambda = 0 and another copy at lambda = 1. + if explicit_dummies: + mol0 = molecule.copy()._toRegularMolecule( + is_lambda1=False, convert_amber_dummies=True, generate_intrascale=True + ) + mol1 = molecule.copy()._toRegularMolecule( + is_lambda1=True, convert_amber_dummies=True, generate_intrascale=True + ) + else: + mol0 = _removeDummies(molecule, False) + mol1 = _removeDummies(molecule, True) + system = (mol0 + mol1).toSystem() + + # We only need to call tiMerge for multi-residue molecules + if molecule.nResidues() == 1: + return system + + # Perform the multi-residue squashing with ParmEd as it is much easier and faster. + with tempfile.TemporaryDirectory() as tempdir: + # Load in ParmEd. + _saveMolecules(f"{tempdir}/temp", mol0 + mol1, "prm7,rst7") + _shutil.move(f"{tempdir}/temp.prm7", f"{tempdir}/temp.parm7") + parm = _pmd.load_file(f"{tempdir}/temp.parm7", xyz=f"{tempdir}/temp.rst7") + + # Determine the molecule masks. + mol_mask0 = f"@1-{mol0.nAtoms()}" + mol_mask1 = f"@{mol0.nAtoms() + 1}-{system.nAtoms()}" + + # Determine the residue masks. + atom0_offset, atom1_offset = 0, mol0.nAtoms() + res_atoms0, res_atoms1 = [], [] + for res0, res1, res01 in zip( + mol0.getResidues(), mol1.getResidues(), molecule.getResidues() + ): + if _is_perturbed(res01) or molecule.nResidues() == 1: + res_atoms0 += list(range(atom0_offset, atom0_offset + res0.nAtoms())) + res_atoms1 += list(range(atom1_offset, atom1_offset + res1.nAtoms())) + atom0_offset += res0.nAtoms() + atom1_offset += res1.nAtoms() + res_mask0 = _amber_mask_from_indices(res_atoms0) + res_mask1 = _amber_mask_from_indices(res_atoms1) + + # Merge the residues. + action = _pmd.tools.tiMerge(parm, mol_mask0, mol_mask1, res_mask0, res_mask1) + action.output = open(_os.devnull, "w") # Avoid some of the spam + action.execute() + + # Reload into BioSimSpace. + # TODO: prm7/rst7 doesn't work for some reason so we need to use gro/top + parm.save(f"{tempdir}/squashed.gro", overwrite=True) + parm.save(f"{tempdir}/squashed.top", overwrite=True) + squashed_mol = _readMolecules( + [f"{tempdir}/squashed.gro", f"{tempdir}/squashed.top"] + ) + + return squashed_mol + + +def _unsquash(system, squashed_system, mapping, **kwargs): + """ + Internal function which converts an alchemical AMBER system where the + perturbed molecules are defined sequentially and updates the coordinates + and velocities of an input unsquashed system. Refer to the _squash() + function documentation to see the structure of the squashed system + relative to the unsquashed one. + + Parameters + ---------- + + system : BioSimSpace._SireWrappers.System + The regular unsquashed system. + + squashed_system : BioSimSpace._SireWrappers.System + The corresponding squashed system. + + mapping : dict(sire.legacy.Mol.MolIdx, sire.legacy.Mol.MolIdx) + The molecule-molecule mapping generated by _squash(). + + kwargs : dict + A dictionary of optional keyword arguments to supply to _unsquash_molecule(). + + Returns + ------- + system : BioSimSpace._SireWrappers.System + The output unsquashed system. + """ + # Create a copy of the original new_system. + new_system = system.copy() + + # Update the unperturbed molecule coordinates in the original new_system + # using the mapping. + if mapping: + new_system._sire_object, _ = _SireIO.updateCoordinatesAndVelocities( + new_system._sire_object, squashed_system._sire_object, mapping + ) + + # From now on we handle all perturbed molecules. + pertmol_idxs = [ + i + for i, molecule in enumerate(new_system.getMolecules()) + if molecule.isPerturbable() + ] + + # Get the molecule mapping and combine it with the lambda=0 molecule + # being prioritised + molecule_mapping0 = _squashed_molecule_mapping(new_system, is_lambda1=False) + molecule_mapping1 = _squashed_molecule_mapping(new_system, is_lambda1=True) + molecule_mapping0_rev = {v: k for k, v in molecule_mapping0.items()} + molecule_mapping1_rev = {v: k for k, v in molecule_mapping1.items()} + molecule_mapping_rev = {**molecule_mapping1_rev, **molecule_mapping0_rev} + molecule_mapping_rev = { + k: v for k, v in molecule_mapping_rev.items() if v in pertmol_idxs + } + + # Update the perturbed molecule coordinates based on the molecule mapping + for merged_idx in set(molecule_mapping_rev.values()): + pertmol = new_system[merged_idx] + squashed_idx0 = molecule_mapping0[merged_idx] + squashed_idx1 = molecule_mapping1[merged_idx] + + if squashed_idx0 == squashed_idx1: + squashed_molecules = squashed_system[squashed_idx0].toSystem() + else: + squashed_molecules = ( + squashed_system[squashed_idx0] + squashed_system[squashed_idx1] + ).toSystem() + + new_pertmol = _unsquash_molecule(pertmol, squashed_molecules, **kwargs) + new_system.updateMolecule(merged_idx, new_pertmol) + + return new_system + + +def _unsquash_molecule(molecule, squashed_molecules, explicit_dummies=False): + """ + This internal function loads the coordinates and velocities of squashed + molecules as defined by the _squash_molecule() function into an unsquashed + merged molecule. + + Parameters + ---------- + + molecule : BioSimSpace._SireWrappers.Molecule + The unsquashed merged molecule whose coordinates and velocities are to be updated. + + squashed_molecules : BioSimSpace._SireWrappers.Molecules + The corresponding squashed molecule(s) whose coordinates are to be used for updating. + + explicit_dummies : bool + Whether to keep the dummy atoms explicit at the endstates or remove them. + + Returns + ------- + + molecule : BioSimSpace._SireWrappers.Molecule + The output updated merged molecule. + """ + # Get the common core atoms + atom_mapping0_common = _squashed_atom_mapping( + molecule, + is_lambda1=False, + explicit_dummies=explicit_dummies, + environment=False, + dummies=False, + ) + atom_mapping1_common = _squashed_atom_mapping( + molecule, + is_lambda1=True, + explicit_dummies=explicit_dummies, + environment=False, + dummies=False, + ) + if set(atom_mapping0_common) != set(atom_mapping1_common): + raise RuntimeError("The MCS atoms don't match between the two endstates") + common_atoms = set(atom_mapping0_common) + + # Get the atom mapping from both endstates + atom_mapping0 = _squashed_atom_mapping( + molecule, is_lambda1=False, explicit_dummies=explicit_dummies + ) + atom_mapping1 = _squashed_atom_mapping( + molecule, is_lambda1=True, explicit_dummies=explicit_dummies + ) + update_velocity = squashed_molecules[0]._sire_object.hasProperty("velocity") + + # Even though the common core of the two molecules should have the same coordinates, + # they might be PBC wrapped differently. + # Here we take the first common core atom and translate the second molecule. + if len(squashed_molecules) == 2: + first_common_atom = list(sorted(common_atoms))[0] + pertatom0 = squashed_molecules.getAtom(atom_mapping0[first_common_atom]) + pertatom1 = squashed_molecules.getAtom(atom_mapping1[first_common_atom]) + pertatom_coords0 = pertatom0._sire_object.property("coordinates") + pertatom_coords1 = pertatom1._sire_object.property("coordinates") + translation_vec = pertatom_coords1 - pertatom_coords0 + + # Update the coordinates and velocities. + siremol = molecule.copy()._sire_object.edit() + for merged_atom_idx in range(molecule.nAtoms()): + # Get the relevant atom indices + merged_atom = siremol.atom(_SireMol.AtomIdx(merged_atom_idx)) + if merged_atom_idx in atom_mapping0: + squashed_atom_idx0 = atom_mapping0[merged_atom_idx] + else: + squashed_atom_idx0 = atom_mapping1[merged_atom_idx] + if merged_atom_idx in atom_mapping1: + squashed_atom_idx1 = atom_mapping1[merged_atom_idx] + apply_translation_vec = True + else: + squashed_atom_idx1 = atom_mapping0[merged_atom_idx] + apply_translation_vec = False + + # Get the coordinates. + squashed_atom0 = squashed_molecules.getAtom(squashed_atom_idx0) + squashed_atom1 = squashed_molecules.getAtom(squashed_atom_idx1) + coordinates0 = squashed_atom0._sire_object.property("coordinates") + coordinates1 = squashed_atom1._sire_object.property("coordinates") + + # Apply the translation if the atom is coming from the second molecule. + if len(squashed_molecules) == 2 and apply_translation_vec: + # This is a dummy atom so we need to translate coordinates0 as well + if squashed_atom_idx0 == squashed_atom_idx1: + coordinates0 -= translation_vec + coordinates1 -= translation_vec + + siremol = merged_atom.setProperty("coordinates0", coordinates0).molecule() + siremol = merged_atom.setProperty("coordinates1", coordinates1).molecule() + + # Update the velocities. + if update_velocity: + velocities0 = squashed_atom0._sire_object.property("velocity") + velocities1 = squashed_atom1._sire_object.property("velocity") + siremol = merged_atom.setProperty("velocity0", velocities0).molecule() + siremol = merged_atom.setProperty("velocity1", velocities1).molecule() + + return _Molecule(siremol.commit()) + + +def _squashed_molecule_mapping(system, is_lambda1=False): + """ + This internal function returns a dictionary whose keys correspond to the + molecule index of the each molecule in the original merged system, and + whose values contain the corresponding index of the same molecule at the + specified endstate in the squashed system. + + Parameters + ---------- + + system : BioSimSpace._SireWrappers.System + The input merged system. + + is_lambda1 : bool + Whether to use the lambda=1 endstate. + + Returns + ------- + + mapping : dict(int, int) + The corresponding molecule mapping. + """ + # Get the perturbable molecules and their corresponding indices. + pertmol_idxs = [i for i, molecule in enumerate(system) if molecule.isPerturbable()] + + # Add them back at the end of the system. This is generally faster than keeping their order the same. + new_indices = list(range(system.nMolecules())) + for pertmol_idx in pertmol_idxs: + new_indices.remove(pertmol_idx) + + # Multi-residue molecules are squashed to one molecule with extra residues. + if system[pertmol_idx].nResidues() > 1: + new_indices.append(pertmol_idx) + # Since we have two squashed molecules, we pick the first one at lambda=0 and the second one at lambda = 1. + elif not is_lambda1: + new_indices.extend([pertmol_idx, None]) + else: + new_indices.extend([None, pertmol_idx]) + + # Create the old molecule index to new molecule index mapping. + mapping = {idx: i for i, idx in enumerate(new_indices) if idx is not None} + + return mapping + + +def _squashed_atom_mapping(system, is_lambda1=False, environment=True, **kwargs): + """ + This internal function returns a dictionary whose keys correspond to the atom + index of the each atom in the original merged system, and whose values + contain the corresponding index of the same atom at the specified endstate + in the squashed system. + + Parameters + ---------- + + system : BioSimSpace._SireWrappers.System + The input merged system. + + is_lambda1 : bool + Whether to use the lambda=1 endstate. + + environment : bool + Whether to include all environment atoms (i.e. ones that are not perturbed). + + kwargs : + Keyword arguments to pass to _squashed_atom_mapping_molecule(). + + Returns + ------- + + mapping : dict(int, int) + The corresponding atom mapping. + """ + if isinstance(system, _Molecule): + return _squashed_atom_mapping( + system.toSystem(), is_lambda1=is_lambda1, environment=environment, **kwargs + ) + + # Both mappings start from 0 and we add all offsets at the end. + atom_mapping = {} + atom_idx, squashed_atom_idx, squashed_atom_idx_perturbed = 0, 0, 0 + squashed_offset = sum(x.nAtoms() for x in system if not x.isPerturbable()) + for molecule in system: + if molecule.isPerturbable(): + residue_atom_mapping, n_squashed_atoms = _squashed_atom_mapping_molecule( + molecule, + offset_merged=atom_idx, + offset_squashed=squashed_offset + squashed_atom_idx_perturbed, + is_lambda1=is_lambda1, + environment=environment, + **kwargs, + ) + atom_mapping.update(residue_atom_mapping) + atom_idx += molecule.nAtoms() + squashed_atom_idx_perturbed += n_squashed_atoms + else: + atom_indices = _np.arange(atom_idx, atom_idx + molecule.nAtoms()) + squashed_atom_indices = _np.arange( + squashed_atom_idx, squashed_atom_idx + molecule.nAtoms() + ) + if environment: + atom_mapping.update(dict(zip(atom_indices, squashed_atom_indices))) + atom_idx += molecule.nAtoms() + squashed_atom_idx += molecule.nAtoms() + + # Convert from NumPy integers to Python integers. + return {int(k): int(v) for k, v in atom_mapping.items()} + + +def _squashed_atom_mapping_molecule( + molecule, + offset_merged=0, + offset_squashed=0, + is_lambda1=False, + environment=True, + common=True, + dummies=True, + explicit_dummies=False, +): + """ + This internal function returns a dictionary whose keys correspond to the atom + index of the each atom in the original merged molecule, and whose values + contain the corresponding index of the same atom at the specified endstate + in the squashed molecule at a particular offset. + + Parameters + ---------- + + molecule : BioSimSpace._SireWrappers.Molecule + The input merged molecule. + + offset_merged : int + The index at which to start the merged atom numbering. + + offset_squashed : int + The index at which to start the squashed atom numbering. + + is_lambda1 : bool + Whether to use the lambda=1 endstate. + + environment : bool + Whether to include all environment atoms (i.e. ones that are not perturbed). + + common : bool + Whether to include all common atoms (i.e. ones that are perturbed but are + not dummies in the endstate of interest). + + dummies : bool + Whether to include all dummy atoms (i.e. ones that are perturbed and are + dummies in the endstate of interest). + + explicit_dummies : bool + Whether to keep the dummy atoms explicit at the endstates or remove them. + + Returns + ------- + + mapping : dict(int, int) + The corresponding atom mapping. + + n_atoms : int + The number of squashed atoms that correspond to the squashed molecule. + """ + if not molecule.isPerturbable(): + if environment: + return { + offset_merged + i: offset_squashed + i for i in range(molecule.nAtoms()) + }, molecule.nAtoms() + else: + return {}, molecule.nAtoms() + + # Both mappings start from 0 and we add all offsets at the end. + mapping, mapping_lambda1 = {}, {} + atom_idx_merged, atom_idx_squashed, atom_idx_squashed_lambda1 = 0, 0, 0 + for residue in molecule.getResidues(): + if not (_is_perturbed(residue) or molecule.nResidues() == 1): + # The residue is not perturbed. + if common: + mapping.update( + { + atom_idx_merged + i: atom_idx_squashed + i + for i in range(residue.nAtoms()) + } + ) + atom_idx_merged += residue.nAtoms() + atom_idx_squashed += residue.nAtoms() + else: + # The residue is perturbed. + + # Determine the dummy and the non-dummy atoms. + types0 = [ + atom._sire_object.property("ambertype0") for atom in residue.getAtoms() + ] + types1 = [ + atom._sire_object.property("ambertype1") for atom in residue.getAtoms() + ] + + if explicit_dummies: + # If both endstates are dummies then we treat them as common core atoms + dummy0 = dummy1 = _np.asarray( + [("du" in x) or ("du" in y) for x, y in zip(types0, types1)] + ) + common0 = common1 = ~dummy0 + in_mol0 = in_mol1 = _np.asarray([True] * residue.nAtoms()) + else: + in_mol0 = _np.asarray(["du" not in x for x in types0]) + in_mol1 = _np.asarray(["du" not in x for x in types1]) + dummy0 = ~in_mol1 + dummy1 = ~in_mol0 + common0 = _np.logical_and(in_mol0, ~dummy0) + common1 = _np.logical_and(in_mol1, ~dummy1) + + ndummy0 = residue.nAtoms() - sum(in_mol1) + ndummy1 = residue.nAtoms() - sum(in_mol0) + ncommon = residue.nAtoms() - ndummy0 - ndummy1 + natoms0 = ncommon + ndummy0 + natoms1 = ncommon + ndummy1 + + # Determine the full mapping indices for the merged and squashed systems. + if not is_lambda1: + atom_indices = _np.arange( + atom_idx_merged, atom_idx_merged + residue.nAtoms() + )[in_mol0] + squashed_atom_indices = _np.arange( + atom_idx_squashed, atom_idx_squashed + natoms0 + ) + mapping_to_update = mapping + else: + atom_indices = _np.arange( + atom_idx_merged, atom_idx_merged + residue.nAtoms() + )[in_mol1] + squashed_atom_indices = _np.arange( + atom_idx_squashed_lambda1, atom_idx_squashed_lambda1 + natoms1 + ) + mapping_to_update = mapping_lambda1 + + # Determine which atoms to return. + in_mol_mask = in_mol1 if is_lambda1 else in_mol0 + common_mask = common1 if is_lambda1 else common0 + dummy_mask = dummy1 if is_lambda1 else dummy0 + update_mask = _np.asarray([False] * atom_indices.size) + + if common: + update_mask = _np.logical_or(update_mask, common_mask[in_mol_mask]) + if dummies: + update_mask = _np.logical_or(update_mask, dummy_mask[in_mol_mask]) + + # Finally update the relevant mapping + mapping_to_update.update( + dict(zip(atom_indices[update_mask], squashed_atom_indices[update_mask])) + ) + + # Increment the offsets and continue. + atom_idx_merged += residue.nAtoms() + atom_idx_squashed += natoms0 + atom_idx_squashed_lambda1 += natoms1 + + # Finally add the appropriate offsets + if explicit_dummies: + all_ndummy1 = 0 + else: + all_ndummy1 = sum( + "du" in x for x in molecule._sire_object.property("ambertype0").toVector() + ) + + offset_squashed_lambda1 = molecule.nAtoms() - all_ndummy1 + res = { + **{offset_merged + k: offset_squashed + v for k, v in mapping.items()}, + **{ + offset_merged + k: offset_squashed + offset_squashed_lambda1 + v + for k, v in mapping_lambda1.items() + }, + } + + return res, atom_idx_squashed + atom_idx_squashed_lambda1 + + +def _is_perturbed(residue): + """ + This determines whether a merged residue is actually perturbed. Note that + it is possible that this function returns false negatives. + + Parameters + ---------- + + residue : BioSimSpace._SireWrappers.Residue + The input residue. + + Returns + ------- + + res : bool + Whether the residue is perturbed. + """ + # If the elements are different, then we are definitely perturbing. + elem0 = [atom._sire_object.property("element0") for atom in residue.getAtoms()] + elem1 = [atom._sire_object.property("element1") for atom in residue.getAtoms()] + return elem0 != elem1 + + +def _amber_mask_from_indices(atom_idxs): + """ + Internal helper function to create an AMBER mask from a list of atom indices. + + Parameters + ---------- + + atom_idxs : [int] + A list of atom indices. + + Returns + ------- + + mask : str + The AMBER mask. + """ + # AMBER has a restriction on the number of characters in the restraint + # mask (not documented) so we can't just use comma-separated atom + # indices. Instead we loop through the indices and use hyphens to + # separate contiguous blocks of indices, e.g. 1-23,34-47,... + + if atom_idxs: + # AMBER masks are 1-indexed, while BioSimSpace indices are 0-indexed. + atom_idxs = [x + 1 for x in sorted(list(set(atom_idxs)))] + if not all(isinstance(x, int) for x in atom_idxs): + raise TypeError("'atom_idxs' must be a list of 'int' types.") + groups = [] + initial_idx = atom_idxs[0] + for prev_idx, curr_idx in _it.zip_longest(atom_idxs, atom_idxs[1:]): + if curr_idx != prev_idx + 1 or curr_idx is None: + if initial_idx == prev_idx: + groups += [str(initial_idx)] + else: + groups += [f"{initial_idx}-{prev_idx}"] + initial_idx = curr_idx + mask = "@" + ",".join(groups) + else: + mask = "" + + return mask diff --git a/python/BioSimSpace/FreeEnergy/_relative.py b/python/BioSimSpace/FreeEnergy/_relative.py index 8db00c5a8..a54a6d707 100644 --- a/python/BioSimSpace/FreeEnergy/_relative.py +++ b/python/BioSimSpace/FreeEnergy/_relative.py @@ -123,7 +123,7 @@ class Relative: """Class for configuring and running relative free-energy perturbation simulations.""" # Create a list of supported molecular dynamics engines. (For running simulations.) - _engines = ["GROMACS", "SOMD"] + _engines = ["AMBER", "GROMACS", "SOMD"] # Create a list of supported molecular dynamics engines. (For analysis.) _engines_analysis = ["AMBER", "GROMACS", "SOMD", "SOMD2"] @@ -135,11 +135,8 @@ def __init__( work_dir=None, engine=None, setup_only=False, - ignore_warnings=False, - show_errors=True, - extra_options={}, - extra_lines=[], property_map={}, + **kwargs, ): """ Constructor. @@ -157,6 +154,9 @@ def __init__( :class:`Protocol.FreeEnergyProduction ` The simulation protocol. + reference_system : :class:`System ` + A reference system to use for position restraints. + work_dir : str The working directory for the free-energy perturbation simulation. @@ -173,27 +173,14 @@ def __init__( can be useful when you don't intend to use BioSimSpace to run the simulation. Note that a 'work_dir' must also be specified. - ignore_warnings : bool - Whether to ignore warnings when generating the binary run file. - This option is specific to GROMACS and will be ignored when a - different molecular dynamics engine is chosen. - - show_errors : bool - Whether to show warning/error messages when generating the binary - run file. This option is specific to GROMACS and will be ignored - when a different molecular dynamics engine is chosen. - - extra_options : dict - A dictionary containing extra options. Overrides the defaults generated - by the protocol. - - extra_lines : [str] - A list of extra lines to put at the end of the configuration file. - property_map : dict A dictionary that maps system "properties" to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { "charge" : "my-charge" } + + kwargs : dict + Additional keyword arguments to pass to the underlying Process + objects. """ # Validate the input. @@ -203,7 +190,7 @@ def __init__( "'system' must be of type 'BioSimSpace._SireWrappers.System'" ) else: - # Store a copy of solvated system. + # Store a copy of the system. self._system = system.copy() # Validate the user specified molecular dynamics engine. @@ -221,19 +208,12 @@ def __init__( "Supported engines are: %r." % ", ".join(self._engines) ) - # Make sure GROMACS is installed if GROMACS engine is selected. - if engine == "GROMACS": - if _gmx_exe is None: - raise _MissingSoftwareError( - "Cannot use GROMACS engine as GROMACS is not installed!" - ) - - # The system must have a perturbable molecule. - if system.nPerturbableMolecules() == 0: - raise ValueError( - "The system must contain a perturbable molecule! " - "Use the 'BioSimSpace.Align' package to map and merge molecules." - ) + # The system must have a perturbable molecule. + if system.nPerturbableMolecules() == 0: + raise ValueError( + "The system must contain a perturbable molecule! " + "Use the 'BioSimSpace.Align' package to map and merge molecules." + ) else: # Use SOMD as a default. @@ -292,36 +272,16 @@ def __init__( # Create the working directory. self._work_dir = _Utils.WorkDir(work_dir) - if not isinstance(ignore_warnings, bool): - raise ValueError("'ignore_warnings' must be of type 'bool.") - self._ignore_warnings = ignore_warnings - - if not isinstance(show_errors, bool): - raise ValueError("'show_errors' must be of type 'bool.") - self._show_errors = show_errors - - # Check the extra options. - if not isinstance(extra_options, dict): - raise TypeError("'extra_options' must be of type 'dict'.") - else: - keys = extra_options.keys() - if not all(isinstance(k, str) for k in keys): - raise TypeError("Keys of 'extra_options' must be of type 'str'.") - self._extra_options = extra_options - - # Check the extra lines. - if not isinstance(extra_lines, list): - raise TypeError("'extra_lines' must be of type 'list'.") - else: - if not all(isinstance(line, str) for line in extra_lines): - raise TypeError("Lines in 'extra_lines' must be of type 'str'.") - self._extra_lines = extra_lines - # Check that the map is valid. if not isinstance(property_map, dict): raise TypeError("'property_map' must be of type 'dict'") self._property_map = property_map + # Validate the kwargs. + if not isinstance(kwargs, dict): + raise TypeError("'kwargs' must be of type 'dict'.") + self._kwargs = kwargs + # Create fake instance methods for 'analyse', 'checkOverlap', # and 'difference'. These pass instance data through to the # staticmethod versions. @@ -2004,7 +1964,7 @@ def _initialise_runner(self, system): processes = [] # Convert to an appropriate water topology. - if self._engine == "SOMD": + if self._engine in ["AMBER", "SOMD"]: system._set_water_topology("AMBER", property_map=self._property_map) elif self._engine == "GROMACS": system._set_water_topology("GROMACS", property_map=self._property_map) @@ -2039,9 +1999,8 @@ def _initialise_runner(self, system): self._protocol, platform=platform, work_dir=first_dir, - extra_options=self._extra_options, - extra_lines=self._extra_lines, property_map=self._property_map, + **self._kwargs, ) if self._setup_only: del first_process @@ -2054,15 +2013,26 @@ def _initialise_runner(self, system): system, self._protocol, work_dir=first_dir, - ignore_warnings=self._ignore_warnings, - show_errors=self._show_errors, - extra_options=self._extra_options, - extra_lines=self._extra_lines, property_map=self._property_map, + **self._kwargs, ) if not self._setup_only: processes.append(first_process) + # AMBER. + elif self._engine == "AMBER": + first_process = _Process.Amber( + system, + self._protocol, + work_dir=first_dir, + property_map=self._property_map, + **self._kwargs, + ) + if self._setup_only: + del first_process + else: + processes.append(first_process) + # Loop over the rest of the lambda values. for x, lam in enumerate(lam_vals[1:]): # Name the directory. @@ -2149,8 +2119,7 @@ def _initialise_runner(self, system): gro, tpr, first_process._exe, - ignore_warnings=self._ignore_warnings, - show_errors=self._show_errors, + **self._kwargs, ) # Create a copy of the process and update the working @@ -2164,6 +2133,7 @@ def _initialise_runner(self, system): process._std_err_file = new_dir + "/gromacs.err" process._gro_file = new_dir + "/gromacs.gro" process._top_file = new_dir + "/gromacs.top" + process._ref_file = new_dir + "/gromacs_ref.gro" process._traj_file = new_dir + "/gromacs.trr" process._config_file = new_dir + "/gromacs.mdp" process._tpr_file = new_dir + "/gromacs.tpr" @@ -2175,29 +2145,46 @@ def _initialise_runner(self, system): ] processes.append(process) + # AMBER. + elif self._engine == "AMBER": + new_config = [] + with open(new_dir + "/amber.cfg", "r") as f: + for line in f: + if "clambda" in line: + new_config.append(" clambda=%s,\n" % lam) + else: + new_config.append(line) + with open(new_dir + "/amber.cfg", "w") as f: + for line in new_config: + f.write(line) + + # Create a copy of the process and update the working + # directory. + if not self._setup_only: + process = _copy.copy(first_process) + process._system = first_process._system.copy() + process._protocol = self._protocol + process._work_dir = new_dir + process._std_out_file = new_dir + "/amber.out" + process._std_err_file = new_dir + "/amber.err" + process._rst_file = new_dir + "/amber.rst7" + process._top_file = new_dir + "/amber.prm7" + process._ref_file = new_dir + "/amber_ref.rst7" + process._traj_file = new_dir + "/amber.nc" + process._config_file = new_dir + "/amber.cfg" + process._nrg_file = new_dir + "/amber.nrg" + process._input_files = [ + process._config_file, + process._rst_file, + process._top_file, + ] + processes.append(process) + if not self._setup_only: # Initialise the process runner. All processes have already been nested # inside the working directory so no need to re-nest. self._runner = _Process.ProcessRunner(processes) - def _update_run_args(self, args): - """ - Internal function to update run arguments for all subprocesses. - - Parameters - ---------- - - args : dict, collections.OrderedDict - A dictionary which contains the new command-line arguments - for the process executable. - """ - - if not isinstance(args, dict): - raise TypeError("'args' must be of type 'dict'") - - for process in self._runner.processes(): - process.setArgs(args) - def getData(name="data", file_link=False, work_dir=None): """ diff --git a/python/BioSimSpace/MD/_md.py b/python/BioSimSpace/MD/_md.py index cc0a9d6f8..d70e8d7ab 100644 --- a/python/BioSimSpace/MD/_md.py +++ b/python/BioSimSpace/MD/_md.py @@ -68,7 +68,7 @@ # Whether each engine supports free energy simulations. This dictionary needs to # be updated as support for different engines is added. _free_energy = { - "AMBER": False, + "AMBER": True, "GROMACS": True, "NAMD": False, "OPENMM": False, @@ -96,7 +96,7 @@ } -def _find_md_engines(system, protocol, engine="auto", gpu_support=False): +def _find_md_engines(system, protocol, engine="AUTO", gpu_support=False): """ Find molecular dynamics engines on the system that support the given protocol and GPU requirements. @@ -173,20 +173,55 @@ def _find_md_engines(system, protocol, engine="auto", gpu_support=False): and (not is_metadynamics or _metadynamics[engine]) and (not is_steering or _steering[engine]) ): - # Check whether this engine exists on the system and has the desired - # GPU support. - for exe, gpu in _md_engines[engine].items(): - # If the user has requested GPU support make sure the engine - # supports it. - if not gpu_support or gpu: - # AMBER - if engine == "AMBER": - # Search AMBERHOME, if set. - if _amber_home is not None: - _exe = "%s/bin/%s" % (_amber_home, exe) - if _os.path.isfile(_exe): + # Special handling for AMBER which has a custom executable finding + # function. + if engine == "AMBER": + from .._Config import Amber as _AmberConfig + from ..Process._amber import _find_exe + + # Is this a vacuum simulation. + is_vacuum = not ( + _AmberConfig.hasBox(system) or _AmberConfig.hasWater(system) + ) + + try: + exe = _find_exe( + is_gpu=gpu_support, + is_free_energy=is_free_energy, + is_vacuum=is_vacuum, + ) + found_engines.append(engine) + found_exes.append(exe) + except: + pass + else: + # Check whether this engine exists on the system and has the desired + # GPU support. + for exe, gpu in _md_engines[engine].items(): + # If the user has requested GPU support make sure the engine + # supports it. + if not gpu_support or gpu: + # GROMACS + if engine == "GROMACS": + if ( + _gmx_exe is not None + and _os.path.basename(_gmx_exe) == exe + ): found_engines.append(engine) - found_exes.append(_exe) + found_exes.append(_gmx_exe) + # OPENMM + elif engine == "OPENMM": + found_engines.append(engine) + found_exes.append(_SireBase.getBinDir() + "/sire_python") + # SOMD + elif engine == "SOMD": + found_engines.append(engine) + if is_free_energy: + found_exes.append( + _SireBase.getBinDir() + "/somd-freenrg" + ) + else: + found_exes.append(_SireBase.getBinDir() + "/somd") # Search system PATH. else: try: @@ -195,30 +230,6 @@ def _find_md_engines(system, protocol, engine="auto", gpu_support=False): found_exes.append(exe) except: pass - # GROMACS - elif engine == "GROMACS": - if _gmx_exe is not None and _os.path.basename(_gmx_exe) == exe: - found_engines.append(engine) - found_exes.append(_gmx_exe) - # OPENMM - elif engine == "OPENMM": - found_engines.append(engine) - found_exes.append(_SireBase.getBinDir() + "/sire_python") - # SOMD - elif engine == "SOMD": - found_engines.append(engine) - if is_free_energy: - found_exes.append(_SireBase.getBinDir() + "/somd-freenrg") - else: - found_exes.append(_SireBase.getBinDir() + "/somd") - # Search system PATH. - else: - try: - exe = _SireBase.findExe(exe).absoluteFilePath() - found_engines.append(engine) - found_exes.append(exe) - except: - pass # No engine was found. if len(found_engines) == 0: diff --git a/python/BioSimSpace/Process/_amber.py b/python/BioSimSpace/Process/_amber.py index 0f19e0e16..466216e87 100644 --- a/python/BioSimSpace/Process/_amber.py +++ b/python/BioSimSpace/Process/_amber.py @@ -43,6 +43,7 @@ from sire.legacy import Mol as _SireMol from .. import _amber_home, _isVerbose +from ..Align._squash import _squash, _unsquash from .._Config import Amber as _AmberConfig from .._Exceptions import IncompatibleError as _IncompatibleError from .._Exceptions import MissingSoftwareError as _MissingSoftwareError @@ -69,13 +70,18 @@ def __init__( self, system, protocol, + reference_system=None, + explicit_dummies=False, exe=None, + is_gpu=False, name="amber", work_dir=None, seed=None, extra_options={}, extra_lines=[], + extra_args={}, property_map={}, + **kwargs, ): """ Constructor. @@ -89,9 +95,20 @@ def __init__( protocol : :class:`Protocol ` The protocol for the AMBER process. + reference_system : :class:`System ` or None + An optional system to use as a source of reference coordinates for position + restraints. It is assumed that this system has the same topology as "system". + If this is None, then "system" is used as a reference. + + explicit_dummies : bool + Whether to keep dummy atoms explicit at alchemical end states, or remove them. + exe : str The full path to the AMBER executable. + is_gpu : bool + Whether to use the GPU accelerated version of AMBER. + name : str The name of the process. @@ -108,52 +125,61 @@ def __init__( extra_lines : [str] A list of extra lines to put at the end of the configuration file. + extra_args : dict + A dictionary of extra command-line arguments to pass to the AMBER executable. + property_map : dict A dictionary that maps system "properties" to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { "charge" : "my-charge" } + + kwargs : dict + Additional keyword arguments. """ # Call the base class constructor. super().__init__( system, protocol, + reference_system=reference_system, name=name, work_dir=work_dir, seed=seed, extra_options=extra_options, extra_lines=extra_lines, + extra_args=extra_args, property_map=property_map, ) - # Catch unsupported protocols. - if isinstance(protocol, _FreeEnergyMixin): - raise _IncompatibleError( - "Unsupported protocol: '%s'" % self._protocol.__class__.__name__ - ) - # Set the package name. self._package_name = "AMBER" # This process can generate trajectory data. self._has_trajectory = True + if not isinstance(is_gpu, bool): + raise TypeError("'is_gpu' must be of type 'bool'") + + # Check whether this is a vacuum simulation. + self._is_vacuum = not ( + _AmberConfig.hasBox(self._system, self._property_map) + or _AmberConfig.hasWater(self._system) + ) + + # Flag to indicate whether the original system has a box. + self._has_box = _AmberConfig.hasBox(self._system, self._property_map) + # If the path to the executable wasn't specified, then search - # for it in $PATH. For now, we'll just search for 'sander', which - # is available free as part of AmberTools. In future, we will - # look for all possible executables in order of preference: pmemd.cuda, - # pmemd, sander, etc., as well as their variants, e.g. pmemd.MPI. + # for it in AMBERHOME and the PATH. if exe is None: - # Search AMBERHOME, if set. - if _amber_home is not None: - exe = "%s/bin/sander" % _amber_home - if _os.path.isfile(exe): - self._exe = exe - else: - raise _MissingSoftwareError( - "'BioSimSpace.Process.Amber' is not supported. " - "Please install AMBER (http://ambermd.org)." - ) + if isinstance(protocol, _FreeEnergyMixin): + is_free_energy = True + else: + is_free_energy = False + + self._exe = _find_exe( + is_gpu=is_gpu, is_free_energy=is_free_energy, is_vacuum=self._is_vacuum + ) else: # Make sure executable exists. if _os.path.isfile(exe): @@ -161,9 +187,48 @@ def __init__( else: raise IOError("AMBER executable doesn't exist: '%s'" % exe) + # Is this a CUDA enabled version of AMBER? + if "cuda" in self._exe.lower(): + self._is_pmemd_cuda = True + self._is_pmemd = False + else: + self._is_pmemd_cuda = False + if "pmemd" in self._exe.lower(): + self._is_pmemd = True + else: + self._is_pmemd = False + + if not isinstance(explicit_dummies, bool): + raise TypeError("'explicit_dummies' must be of type 'bool'") + self._explicit_dummies = explicit_dummies + # Initialise the energy dictionary and header. self._stdout_dict = _process._MultiDict() + # Initialise dictionaries to hold stdout records for all possible + # regions. For regular simulations there will be one, for free-energy + # simulations there can be up to four, i.e. one for each of the TI regions + # and one for the soft-core part of the system in each region, if present. + # The order of the dictionaries is: + # - TI region 1 + # - TI region 1 (soft-core part) + # - TI region 2 + # - TI region 2 (soft-core part) + self._stdout_dict = [ + _process._MultiDict(), + _process._MultiDict(), + _process._MultiDict(), + _process._MultiDict(), + ] + + # Initialise mappings between "universal" stdout keys, and the actual + # record key used for the different regions (and soft-core parts) from + # in the AMBER output. Ordering is the same as for the stdout_dicts above. + self._stdout_key = [{}, {}, {}, {}] + + # Flag for the current record region in the AMBER output file. + self._current_region = 0 + # Initialise log file parsing flags. self._has_results = False self._finished_results = False @@ -172,6 +237,7 @@ def __init__( # The names of the input files. self._rst_file = "%s/%s.rst7" % (self._work_dir, name) self._top_file = "%s/%s.prm7" % (self._work_dir, name) + self._ref_file = "%s/%s_ref.rst7" % (self._work_dir, name) # The name of the trajectory file. self._traj_file = "%s/%s.nc" % (self._work_dir, name) @@ -182,10 +248,14 @@ def __init__( # Create the list of input files. self._input_files = [self._config_file, self._rst_file, self._top_file] + # Add the reference file if there are position restraints. + if self._protocol.getRestraint() is not None: + self._input_files.append(self._ref_file) + # Now set up the working directory for the process. - self._setup() + self._setup(**kwargs) - def _setup(self): + def _setup(self, **kwargs): """Setup the input files and working directory ready for simulation.""" # Create the input files... @@ -195,9 +265,63 @@ def _setup(self): # Convert the water model topology so that it matches the AMBER naming convention. system._set_water_topology("AMBER", property_map=self._property_map) + self._reference_system._set_water_topology( + "AMBER", property_map=self._property_map + ) - # Check for perturbable molecules and convert to the chosen end state. - system = self._checkPerturbable(system) + # Create the squashed system. + if isinstance(self._protocol, _FreeEnergyMixin): + # Check that the system contains a perturbable molecule. + if self._system.nPerturbableMolecules() == 0: + raise ValueError( + "'BioSimSpace.Protocol.FreeEnergy' requires a " + "perturbable molecule!" + ) + + # If this is vacuum simulation with pmemd.cuda then + # we need to add a simulation box. + if self._is_vacuum and self._is_pmemd_cuda: + # Get the existing box information. + box, _ = system.getBox() + + # We need to add a box. + if box is None: + from ..Box import cubic as _cubic + from ..Units.Length import angstrom as _angstrom + + # Get the bounding box of the system. + box_min, box_max = system.getAxisAlignedBoundingBox() + + # Work out the box size from the difference in the coordinates. + box_size = [y - x for x, y in zip(box_min, box_max)] + + # Work out the size of the box assuming an 8 Angstrom non-bonded cutoff. + padding = 8 * _angstrom + box_length = max(box_size) + padding + # Small box fix. Should be patched in future versions of pmemd.cuda. + if box_length < 30 * _angstrom: + box_length = 30 * _angstrom + + # Set the simulation box. + system.setBox(*_cubic(box_length)) + + # Apply SOMD1 compatibility to the perturbation. + if ( + "somd1_compatibility" in kwargs + and kwargs.get("somd1_compatibility") is True + ): + from ._somd import _somd1_compatibility + + system = _somd1_compatibility(system) + + system, self._mapping = _squash( + system, explicit_dummies=self._explicit_dummies + ) + self._squashed_system = system + + else: + # Check for perturbable molecules and convert to the chosen end state. + system = self._checkPerturbable(system) # RST file (coordinates). try: @@ -210,6 +334,19 @@ def _setup(self): else: raise IOError(msg) from None + # Reference file for position restraints. + try: + file = _os.path.splitext(self._ref_file)[0] + _IO.saveMolecules( + file, self._reference_system, "rst7", property_map=self._property_map + ) + except Exception as e: + msg = "Failed to write reference system to 'RST7' format." + if _isVerbose(): + raise IOError(msg) from e + else: + raise IOError(msg) from None + # PRM file (topology). try: file = _os.path.splitext(self._top_file)[0] @@ -240,12 +377,6 @@ def _setup(self): def _generate_config(self): """Generate AMBER configuration file strings.""" - # Work out whether we're generating a config for PMEMD. - if "pmemd" in self._exe.lower(): - is_pmemd = True - else: - is_pmemd = False - extra_options = self._extra_options.copy() extra_lines = self._extra_lines.copy() @@ -287,7 +418,11 @@ def _generate_config(self): # Create the configuration. self.setConfig( amber_config.createConfig( - is_pmemd=is_pmemd, extra_options=extra_options, extra_lines=extra_lines + is_pmemd=self._is_pmemd, + is_pmemd_cuda=self._is_pmemd_cuda, + explicit_dummies=self._explicit_dummies, + extra_options=extra_options, + extra_lines=extra_lines, ) ) @@ -315,12 +450,16 @@ def _generate_args(self): # Append a reference file if a position restraint is specified. if isinstance(self._protocol, _PositionRestraintMixin): if self._protocol.getRestraint() is not None: - self.setArg("-ref", "%s.rst7" % self._name) + self.setArg("-ref", "%s_ref.rst7" % self._name) # Append a trajectory file if this anything other than a minimisation. if not isinstance(self._protocol, _Protocol.Minimisation): self.setArg("-x", "%s.nc" % self._name) + # Add the extra arguments. + for key, value in self._extra_args.items(): + self.setArg(key, value) + def start(self): """ Start the AMBER process. @@ -422,31 +561,60 @@ def getSystem(self, block="AUTO"): # Create a copy of the existing system object. old_system = self._system.copy() - # Update the coordinates and velocities and return a mapping between - # the molecule indices in the two systems. - sire_system, mapping = _SireIO.updateCoordinatesAndVelocities( - old_system._sire_object, - new_system._sire_object, - self._mapping, - is_lambda1, - self._property_map, - self._property_map, - ) + if isinstance(self._protocol, _FreeEnergyMixin): + # Udpate the coordinates and velocities and return a mapping between + # the molecule indices in the two systems. + mapping = { + _SireMol.MolIdx(x): _SireMol.MolIdx(x) + for x in range(0, self._squashed_system.nMolecules()) + } + ( + self._squashed_system._sire_object, + _, + ) = _SireIO.updateCoordinatesAndVelocities( + self._squashed_system._sire_object, + new_system._sire_object, + mapping, + is_lambda1, + self._property_map, + self._property_map, + ) - # Update the underlying Sire object. - old_system._sire_object = sire_system + # Update the unsquashed system based on the updated squashed system. + old_system = _unsquash( + old_system, + self._squashed_system, + self._mapping, + explicit_dummies=self._explicit_dummies, + ) - # Store the mapping between the MolIdx in both systems so we don't - # need to recompute it next time. - self._mapping = mapping + else: + # Update the coordinates and velocities and return a mapping between + # the molecule indices in the two systems. + sire_system, mapping = _SireIO.updateCoordinatesAndVelocities( + old_system._sire_object, + new_system._sire_object, + self._mapping, + is_lambda1, + self._property_map, + self._property_map, + ) + + # Update the underlying Sire object. + old_system._sire_object = sire_system + + # Store the mapping between the MolIdx in both systems so we don't + # need to recompute it next time. + self._mapping = mapping # Update the box information in the original system. - if "space" in new_system._sire_object.propertyKeys(): - box = new_system._sire_object.property("space") - if box.isPeriodic(): - old_system._sire_object.setProperty( - self._property_map.get("space", "space"), box - ) + if self._has_box: + if "space" in new_system._sire_object.propertyKeys(): + box = new_system._sire_object.property("space") + if box.isPeriodic(): + old_system._sire_object.setProperty( + self._property_map.get("space", "space"), box + ) return old_system @@ -569,18 +737,77 @@ def getFrame(self, index): self._mapping = mapping # Update the box information in the original system. - if "space" in new_system._sire_object.propertyKeys(): - box = new_system._sire_object.property("space") - old_system._sire_object.setProperty( - self._property_map.get("space", "space"), box - ) + if self._has_box: + if "space" in new_system._sire_object.propertyKeys(): + box = new_system._sire_object.property("space") + old_system._sire_object.setProperty( + self._property_map.get("space", "space"), box + ) return old_system except: return None - def getRecord(self, key, time_series=False, unit=None, block="AUTO"): + def getRecordKey(self, record, region=0, soft_core=False): + """ + Parameters + ---------- + + record : str + The record used in the AMBER standard output, e.g. 'TEMP(K)'. + Please consult the current AMBER manual for details: + https://ambermd.org/Manuals.php + + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + + Returns + ------- + + key : str + The universal record key that can be used with getRecord. + """ + + # Validate the record string. + if not isinstance(record, str): + raise TypeError("'record' must be of type 'str'") + + # Validate the region. + if not isinstance(region, int): + raise TypeError("'region' must be of type 'int'") + else: + if region < 0 or region > 1: + raise ValueError("'region' must be in range [0, 1]") + + # Validate the soft-core flag. + if not isinstance(soft_core, bool): + raise TypeError("'soft_core' must be of type 'bool'.") + + # Convert to the full index. + idx = 2 * region + int(soft_core) + + # Strip whitespace from the beginning and end of the record and convert + # to upper case. + cleaned_record = record.strip().upper() + + # Make sure the record exists in the key mapping. + if not cleaned_record in self._stdout_key[idx].values(): + raise ValueError(f"No key found for record '{record}'") + + return list(self._stdout_key[idx].keys())[ + list(self._stdout_key[idx].values()).index(cleaned_record) + ] + + def getRecord( + self, key, time_series=False, unit=None, region=0, soft_core=False, block="AUTO" + ): """ Get a record from the stdout dictionary. @@ -588,7 +815,10 @@ def getRecord(self, key, time_series=False, unit=None, block="AUTO"): ---------- key : str - The record key. + A universal record key based on the key used in the AMBER standard + output. Use 'getRecordKey(record)` to generate the key. The records + are those used in the AMBER standard output, e.g. 'TEMP(K)'. Please + consult the current AMBER manual for details: https://ambermd.org/Manuals.php time_series : bool Whether to return a list of time series records. @@ -596,6 +826,15 @@ def getRecord(self, key, time_series=False, unit=None, block="AUTO"): unit : :class:`Unit ` The unit to convert the record to. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -617,10 +856,16 @@ def getRecord(self, key, time_series=False, unit=None, block="AUTO"): _warnings.warn("The process exited with an error!") return self._get_stdout_record( - key.strip().upper(), time_series=time_series, unit=unit + key.strip().upper(), + time_series=time_series, + unit=unit, + region=region, + soft_core=soft_core, ) - def getCurrentRecord(self, key, time_series=False, unit=None): + def getCurrentRecord( + self, key, time_series=False, unit=None, region=0, soft_core=False + ): """ Get a current record from the stdout dictionary. @@ -628,7 +873,10 @@ def getCurrentRecord(self, key, time_series=False, unit=None): ---------- key : str - The record key. + A universal record key based on the key used in the AMBER standard + output. Use 'getRecordKey(record)` to generate the key. The records + are those used in the AMBER standard output, e.g. 'TEMP(K)'. Please + consult the current AMBER manual for details: https://ambermd.org/Manuals.php time_series : bool Whether to return a list of time series records. @@ -636,6 +884,15 @@ def getCurrentRecord(self, key, time_series=False, unit=None): unit : :class:`Unit ` The unit to convert the record to. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- @@ -648,16 +905,29 @@ def getCurrentRecord(self, key, time_series=False, unit=None): _warnings.warn("The process exited with an error!") return self._get_stdout_record( - key.strip().upper(), time_series=time_series, unit=unit + key.strip().upper(), + time_series=time_series, + unit=unit, + region=region, + soft_core=soft_core, ) - def getRecords(self, block="AUTO"): + def getRecords(self, region=0, soft_core=False, block="AUTO"): """ Return the dictionary of stdout time-series records. Parameters ---------- + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -668,6 +938,20 @@ def getRecords(self, block="AUTO"): The dictionary of time-series records. """ + # Validate the region. + if not isinstance(region, int): + raise TypeError("'region' must be of type 'int'") + else: + if region < 0 or region > 1: + raise ValueError("'region' must be in range [0, 1]") + + # Validate the soft-core flag. + if not isinstance(soft_core, bool): + raise TypeError("'soft_core' must be of type 'bool'.") + + # Convert to the full index, region + soft_core. + idx = 2 * region + int(soft_core) + # Wait for the process to finish. if block is True: self.wait() @@ -679,21 +963,34 @@ def getRecords(self, block="AUTO"): _warnings.warn("The process exited with an error!") self.stdout(0) - return self._stdout_dict.copy() - def getCurrentRecords(self): + return self._stdout_dict[idx].copy() + + def getCurrentRecords(self, region=0, soft_core=False): """ Return the current dictionary of stdout time-series records. + Parameters + ---------- + + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- records : :class:`MultiDict ` The dictionary of time-series records. """ - return self.getRecords(block=False) + return self.getRecords(region=region, soft_core=soft_core, block=False) - def getTime(self, time_series=False, block="AUTO"): + def getTime(self, time_series=False, region=0, soft_core=False, block="AUTO"): """ Get the simulation time. @@ -703,6 +1000,15 @@ def getTime(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -718,7 +1024,14 @@ def getTime(self, time_series=False, block="AUTO"): return None # Get the list of time steps. - time_steps = self.getRecord("TIME(PS)", time_series=time_series, block=block) + time_steps = self.getRecord( + "TIME(PS)", + time_series=time_series, + unit=None, + region=region, + soft_core=soft_core, + block=block, + ) # Convert from picoseconds to nanoseconds. if time_steps is not None: @@ -729,7 +1042,7 @@ def getTime(self, time_series=False, block="AUTO"): else: return (time_steps * _Units.Time.picosecond)._to_default_unit() - def getCurrentTime(self, time_series=False): + def getCurrentTime(self, time_series=False, region=0, soft_core=False): """ Get the current simulation time. @@ -739,15 +1052,26 @@ def getCurrentTime(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- time : :class:`Time ` The current simulation time in nanoseconds. """ - return self.getTime(time_series, block=False) + return self.getTime( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getStep(self, time_series=False, block="AUTO"): + def getStep(self, time_series=False, region=0, soft_core=False, block="AUTO"): """ Get the number of integration steps. @@ -757,6 +1081,15 @@ def getStep(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -766,9 +1099,16 @@ def getStep(self, time_series=False, block="AUTO"): step : int The current number of integration steps. """ - return self.getRecord("NSTEP", time_series=time_series, block=block) + return self.getRecord( + "NSTEP", + time_series=time_series, + unit=None, + region=region, + soft_core=soft_core, + block=block, + ) - def getCurrentStep(self, time_series=False): + def getCurrentStep(self, time_series=False, region=0, soft_core=False): """ Get the current number of integration steps. @@ -778,15 +1118,26 @@ def getCurrentStep(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- step : int The current number of integration steps. """ - return self.getStep(time_series, block=False) + return self.getStep( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getBondEnergy(self, time_series=False, block="AUTO"): + def getBondEnergy(self, time_series=False, region=0, soft_core=False, block="AUTO"): """ Get the bond energy. @@ -796,6 +1147,10 @@ def getBondEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -809,10 +1164,12 @@ def getBondEnergy(self, time_series=False, block="AUTO"): "BOND", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentBondEnergy(self, time_series=False): + def getCurrentBondEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current bond energy. @@ -822,15 +1179,28 @@ def getCurrentBondEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The bond energy. """ - return self.getBondEnergy(time_series, block=False) + return self.getBondEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getAngleEnergy(self, time_series=False, block="AUTO"): + def getAngleEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the angle energy. @@ -840,6 +1210,15 @@ def getAngleEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -853,10 +1232,12 @@ def getAngleEnergy(self, time_series=False, block="AUTO"): "ANGLE", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentAngleEnergy(self, time_series=False): + def getCurrentAngleEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current angle energy. @@ -866,15 +1247,28 @@ def getCurrentAngleEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The angle energy. """ - return self.getAngleEnergy(time_series, block=False) + return self.getAngleEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getDihedralEnergy(self, time_series=False, block="AUTO"): + def getDihedralEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the total dihedral energy (proper + improper). @@ -884,6 +1278,15 @@ def getDihedralEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -897,10 +1300,12 @@ def getDihedralEnergy(self, time_series=False, block="AUTO"): "DIHED", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentDihedralEnergy(self, time_series=False): + def getCurrentDihedralEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current total dihedral energy (proper + improper). @@ -910,15 +1315,28 @@ def getCurrentDihedralEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The total dihedral energy. """ - return self.getDihedralEnergy(time_series, block=False) + return self.getDihedralEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getElectrostaticEnergy(self, time_series=False, block="AUTO"): + def getElectrostaticEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the electrostatic energy. @@ -928,6 +1346,15 @@ def getElectrostaticEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -938,13 +1365,17 @@ def getElectrostaticEnergy(self, time_series=False, block="AUTO"): The electrostatic energy. """ return self.getRecord( - "EELEC", + "EEL", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentElectrostaticEnergy(self, time_series=False): + def getCurrentElectrostaticEnergy( + self, time_series=False, region=0, soft_core=False + ): """ Get the current dihedral energy. @@ -954,15 +1385,28 @@ def getCurrentElectrostaticEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The electrostatic energy. """ - return self.getElectrostaticEnergy(time_series, block=False) + return self.getElectrostaticEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getElectrostaticEnergy14(self, time_series=False, block="AUTO"): + def getElectrostaticEnergy14( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the electrostatic energy between atoms 1 and 4. @@ -972,6 +1416,15 @@ def getElectrostaticEnergy14(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -982,13 +1435,17 @@ def getElectrostaticEnergy14(self, time_series=False, block="AUTO"): The electrostatic energy between atoms 1 and 4. """ return self.getRecord( - "1-4 EEL", + "14EEL", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentElectrostaticEnergy14(self, time_series=False): + def getCurrentElectrostaticEnergy14( + self, time_series=False, region=0, soft_core=False + ): """ Get the current electrostatic energy between atoms 1 and 4. @@ -998,15 +1455,28 @@ def getCurrentElectrostaticEnergy14(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The electrostatic energy between atoms 1 and 4. """ - return self.getElectrostaticEnergy14(time_series, block=False) + return self.getElectrostaticEnergy14( + time_series=time_series, region=region, soft_core=False, block=False + ) - def getVanDerWaalsEnergy(self, time_series=False, block="AUTO"): + def getVanDerWaalsEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the Van der Vaals energy. @@ -1016,6 +1486,15 @@ def getVanDerWaalsEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1026,13 +1505,15 @@ def getVanDerWaalsEnergy(self, time_series=False, block="AUTO"): The Van der Vaals energy. """ return self.getRecord( - "VDWAALS", + "VDW", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentVanDerWaalsEnergy(self, time_series=False): + def getCurrentVanDerWaalsEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current Van der Vaals energy. @@ -1042,15 +1523,98 @@ def getCurrentVanDerWaalsEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The Van der Vaals energy. """ - return self.getVanDerWaalsEnergy(time_series, block=False) + return self.getVanDerWaalsEnergy( + time_series=time_series, block=False, region=region, soft_core=soft_core + ) + + def getVanDerWaalsEnergy14( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): + """ + Get the Van der Vaals energy between atoms 1 and 4. + + Parameters + ---------- + + time_series : bool + Whether to return a list of time series records. + + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + + block : bool + Whether to block until the process has finished running. + + Returns + ------- + + energy : :class:`Energy ` + The Van der Vaals energy between atoms 1 and 4. + """ + return self.getRecord( + "14VDW", + time_series=time_series, + unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, + block=block, + ) - def getHydrogenBondEnergy(self, time_series=False, block="AUTO"): + def getCurrentVanDerWaalsEnergy14( + self, time_series=False, region=0, soft_core=False + ): + """ + Get the current Van der Vaals energy between atoms 1 and 4. + + Parameters + ---------- + + time_series : bool + Whether to return a list of time series records. + + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + + Returns + ------- + + energy : :class:`Energy ` + The Van der Vaals energy between atoms 1 and 4. + """ + return self.getVanDerWaalsEnergy( + time_series=time_series, block=False, region=region, soft_core=soft_core + ) + + def getHydrogenBondEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the hydrogen bond energy. @@ -1060,6 +1624,15 @@ def getHydrogenBondEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1073,10 +1646,14 @@ def getHydrogenBondEnergy(self, time_series=False, block="AUTO"): "EHBOND", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentHydrogenBondEnergy(self, time_series=False): + def getCurrentHydrogenBondEnergy( + self, time_series=False, region=0, soft_core=False + ): """ Get the current hydrogen bond energy. @@ -1086,15 +1663,28 @@ def getCurrentHydrogenBondEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The hydrogen bond energy. """ - return self.getHydrogenBondEnergy(time_series, block=False) + return self.getHydrogenBondEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getRestraintEnergy(self, time_series=False, block="AUTO"): + def getRestraintEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the restraint energy. @@ -1104,6 +1694,15 @@ def getRestraintEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1117,10 +1716,12 @@ def getRestraintEnergy(self, time_series=False, block="AUTO"): "RESTRAINT", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentRestraintEnergy(self, time_series=False): + def getCurrentRestraintEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current restraint energy. @@ -1130,6 +1731,15 @@ def getCurrentRestraintEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1139,9 +1749,13 @@ def getCurrentRestraintEnergy(self, time_series=False): energy : :class:`Energy ` The restraint energy. """ - return self.getRestraintEnergy(time_series, block=False) + return self.getRestraintEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getPotentialEnergy(self, time_series=False, block="AUTO"): + def getPotentialEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the potential energy. @@ -1151,6 +1765,15 @@ def getPotentialEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1164,10 +1787,12 @@ def getPotentialEnergy(self, time_series=False, block="AUTO"): "EPTOT", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentPotentialEnergy(self, time_series=False): + def getCurrentPotentialEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current potential energy. @@ -1177,15 +1802,28 @@ def getCurrentPotentialEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The potential energy. """ - return self.getPotentialEnergy(time_series, block=False) + return self.getPotentialEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getKineticEnergy(self, time_series=False, block="AUTO"): + def getKineticEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the kinetic energy. @@ -1195,6 +1833,15 @@ def getKineticEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1208,10 +1855,12 @@ def getKineticEnergy(self, time_series=False, block="AUTO"): "EKTOT", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentKineticEnergy(self, time_series=False): + def getCurrentKineticEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current kinetic energy. @@ -1221,15 +1870,28 @@ def getCurrentKineticEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The kinetic energy. """ - return self.getKineticEnergy(time_series, block=False) + return self.getKineticEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getNonBondedEnergy14(self, time_series=False, block="AUTO"): + def getNonBondedEnergy14( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the non-bonded energy between atoms 1 and 4. @@ -1239,6 +1901,15 @@ def getNonBondedEnergy14(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1249,13 +1920,15 @@ def getNonBondedEnergy14(self, time_series=False, block="AUTO"): The non-bonded energy between atoms 1 and 4. """ return self.getRecord( - "1-4 NB", + "14NB", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentNonBondedEnergy14(self, time_series=False): + def getCurrentNonBondedEnergy14(self, time_series=False, region=0, soft_core=False): """ Get the current non-bonded energy between atoms 1 and 4. @@ -1265,15 +1938,28 @@ def getCurrentNonBondedEnergy14(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The non-bonded energy between atoms 1 and 4. """ - return self.getNonBondedEnergy14(time_series, block=False) + return self.getNonBondedEnergy14( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getTotalEnergy(self, time_series=False, block="AUTO"): + def getTotalEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the total energy. @@ -1283,6 +1969,15 @@ def getTotalEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1292,11 +1987,27 @@ def getTotalEnergy(self, time_series=False, block="AUTO"): energy : :class:`Energy ` The total energy. """ - if isinstance(self._protocol, _Protocol.Minimisation): + + if not isinstance(region, int): + raise TypeError("'region' must be of type 'int'") + else: + if region < 0 or region > 1: + raise ValueError("'region' must be in range [0, 1]") + + # Validate the soft-core flag. + if not isinstance(soft_core, bool): + raise TypeError("'soft_core' must be of type 'bool'.") + + # Convert to the full index, region + soft_core. + idx = 2 * region + int(soft_core) + + if isinstance(self._protocol, _Protocol.Minimisation) and not soft_core: return self.getRecord( "ENERGY", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) else: @@ -1304,10 +2015,12 @@ def getTotalEnergy(self, time_series=False, block="AUTO"): "ETOT", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentTotalEnergy(self, time_series=False): + def getCurrentTotalEnergy(self, time_series=False, region=0, soft_core=False): """ Get the current total energy. @@ -1317,15 +2030,28 @@ def getCurrentTotalEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The total energy. """ - return self.getTotalEnergy(time_series, block=False) + return self.getTotalEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getCentreOfMassKineticEnergy(self, time_series=False, block="AUTO"): + def getCentreOfMassKineticEnergy( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the kinetic energy of the centre of mass in translation. @@ -1335,6 +2061,15 @@ def getCentreOfMassKineticEnergy(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1348,10 +2083,14 @@ def getCentreOfMassKineticEnergy(self, time_series=False, block="AUTO"): "EKCMT", time_series=time_series, unit=_Units.Energy.kcal_per_mol, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentCentreOfMassKineticEnergy(self, time_series=False): + def getCurrentCentreOfMassKineticEnergy( + self, time_series=False, region=0, soft_core=False + ): """ Get the current kinetic energy of the centre of mass in translation. @@ -1361,15 +2100,26 @@ def getCurrentCentreOfMassKineticEnergy(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- energy : :class:`Energy ` The centre of mass kinetic energy. """ - return self.getCentreOfMassKineticEnergy(time_series, block=False) + return self.getCentreOfMassKineticEnergy( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getVirial(self, time_series=False, block="AUTO"): + def getVirial(self, time_series=False, region=0, soft_core=False, block="AUTO"): """ Get the virial. @@ -1379,6 +2129,15 @@ def getVirial(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1388,9 +2147,15 @@ def getVirial(self, time_series=False, block="AUTO"): virial : float The virial. """ - return self.getRecord("VIRIAL", time_series=time_series, block=block) + return self.getRecord( + "VIRIAL", + time_series=time_series, + region=region, + soft_core=soft_core, + block=block, + ) - def getCurrentVirial(self, time_series=False): + def getCurrentVirial(self, time_series=False, region=0, soft_core=False): """ Get the current virial. @@ -1400,15 +2165,28 @@ def getCurrentVirial(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- virial : float The virial. """ - return self.getVirial(time_series, block=False) + return self.getVirial( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getTemperature(self, time_series=False, block="AUTO"): + def getTemperature( + self, time_series=False, region=0, soft_core=False, block="AUTO" + ): """ Get the temperature. @@ -1418,6 +2196,15 @@ def getTemperature(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1431,10 +2218,12 @@ def getTemperature(self, time_series=False, block="AUTO"): "TEMP(K)", time_series=time_series, unit=_Units.Temperature.kelvin, + region=region, + soft_core=soft_core, block=block, ) - def getCurrentTemperature(self, time_series=False): + def getCurrentTemperature(self, time_series=False, region=0, soft_core=False): """ Get the current temperature. @@ -1444,15 +2233,26 @@ def getCurrentTemperature(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- temperature : :class:`Temperature ` The temperature. """ - return self.getTemperature(time_series, block=False) + return self.getTemperature( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getPressure(self, time_series=False, block="AUTO"): + def getPressure(self, time_series=False, region=0, soft_core=False, block="AUTO"): """ Get the pressure. @@ -1462,6 +2262,15 @@ def getPressure(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1472,10 +2281,15 @@ def getPressure(self, time_series=False, block="AUTO"): The pressure. """ return self.getRecord( - "PRESS", time_series=time_series, unit=_Units.Pressure.bar, block=block + "PRESS", + time_series=time_series, + unit=_Units.Pressure.bar, + region=region, + soft_core=soft_core, + block=block, ) - def getCurrentPressure(self, time_series=False): + def getCurrentPressure(self, time_series=False, region=0, soft_core=False): """ Get the current pressure. @@ -1485,15 +2299,26 @@ def getCurrentPressure(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- pressure : :class:`Pressure ` The pressure. """ - return self.getPressure(time_series, block=False) + return self.getPressure( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getVolume(self, time_series=False, block="AUTO"): + def getVolume(self, time_series=False, region=0, soft_core=False, block="AUTO"): """ Get the volume. @@ -1503,6 +2328,15 @@ def getVolume(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1513,10 +2347,15 @@ def getVolume(self, time_series=False, block="AUTO"): The volume. """ return self.getRecord( - "VOLUME", time_series=time_series, unit=_Units.Volume.angstrom3, block=block + "VOLUME", + time_series=time_series, + unit=_Units.Volume.angstrom3, + region=region, + soft_core=soft_core, + block=block, ) - def getCurrentVolume(self, time_series=False): + def getCurrentVolume(self, time_series=False, region=0, soft_core=False): """ Get the current volume. @@ -1526,15 +2365,26 @@ def getCurrentVolume(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- volume : :class:`Volume ` The volume. """ - return self.getVolume(time_series, block=False) + return self.getVolume( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) - def getDensity(self, time_series=False, block="AUTO"): + def getDensity(self, time_series=False, region=0, soft_core=False, block="AUTO"): """ Get the density. @@ -1544,6 +2394,15 @@ def getDensity(self, time_series=False, block="AUTO"): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + block : bool Whether to block until the process has finished running. @@ -1553,9 +2412,15 @@ def getDensity(self, time_series=False, block="AUTO"): density : float The density. """ - return self.getRecord("DENSITY", time_series=time_series, block=block) + return self.getRecord( + "DENSITY", + time_series=time_series, + region=region, + soft_core=soft_core, + block=block, + ) - def getCurrentDensity(self, time_series=False): + def getCurrentDensity(self, time_series=False, region=0, soft_core=False): """ Get the current density. @@ -1565,13 +2430,89 @@ def getCurrentDensity(self, time_series=False): time_series : bool Whether to return a list of time series records. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- density : float The density. """ - return self.getDensity(time_series, block=False) + return self.getDensity( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) + + def getDVDL(self, time_series=False, region=0, soft_core=False, block="AUTO"): + """ + Get the gradient of the total energy with respect to lambda. + + Parameters + ---------- + + time_series : bool + Whether to return a list of time series records. + + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + + block : bool + Whether to block until the process has finished running. + + Returns + ------- + + dv_dl : float + The gradient of the total energy with respect to lambda. + """ + return self.getRecord( + "DVDL", + time_series=time_series, + region=region, + soft_core=soft_core, + block=block, + ) + + def getCurrentDVDL(self, time_series=False, region=0, soft_core=False): + """ + Get the current gradient of the total energy with respect to lambda. + + Parameters + ---------- + + time_series : bool + Whether to return a list of time series records. + + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + + Returns + ------- + + dv_dl : float + The current gradient of the total energy with respect to lambda. + """ + return self.getDVDL( + time_series=time_series, region=region, soft_core=soft_core, block=False + ) def stdout(self, n=10): """ @@ -1596,15 +2537,39 @@ def stdout(self, n=10): self._stdout.append(line.rstrip()) line = line.strip() + # Swap dictionary based on the protocol and the degre of freedom to + # which the next block of records correspond. + if isinstance(self._protocol, _FreeEnergyMixin): + if "TI region 1" in line: + self._current_region = 0 + elif "TI region 2" in line: + self._current_region = 2 + elif "Softcore part" in line and self._current_region == 0: + self._current_region = 1 + elif "Softcore part" in line and self._current_region == 2: + self._current_region = 3 + elif "Detailed TI info" in line: + # This flags that we should skip records until the start of + # the next set for the first TI region. + self._current_region = 4 + # Default stdout dictionary. + else: + self._current_region = 0 + + # Continue if we are ignoring this record block. + if self._current_region == 4: + continue + + stdout_dict = self._stdout_dict[self._current_region] + stdout_key = self._stdout_key[self._current_region] + # Skip empty lines and summary reports. - if ( - len(line) > 0 - and line[0] != "|" - and line[0] != "-" - and not line.startswith("EAMBER") - ): + if len(line) > 0 and line[0] != "|" and line[0] != "-": + # Skip EAMBER records. + if "EAMBER (non-restraint)" in line: + continue # Flag that we've started recording results. - if not self._has_results and line.startswith("NSTEP"): + elif not self._has_results and line.startswith("NSTEP"): self._has_results = True self._finished_results = False # Flag that we've finished recording results. @@ -1613,7 +2578,7 @@ def stdout(self, n=10): # Parse the results. if self._has_results and not self._finished_results: - # The output format is different for minimisation protocols. + # The first line of output has different formatting for minimisation protocols. if isinstance(self._protocol, _Protocol.Minimisation): # No equals sign in the line. if "NSTEP" in line and "=" not in line: @@ -1633,32 +2598,58 @@ def stdout(self, n=10): # The file hasn't been updated. if ( - "NSTEP" in self._stdout_dict - and data[0] == self._stdout_dict["NSTEP"][-1] + "NSTEP" in stdout_dict + and data[0] == stdout_dict["NSTEP"][-1] ): self._finished_results = True continue # Add the timestep and energy records to the dictionary. - self._stdout_dict["NSTEP"] = data[0] - self._stdout_dict["ENERGY"] = data[1] + stdout_dict["NSTEP"] = data[0] + stdout_dict["ENERGY"] = data[1] + + # Add the keys to the mapping + stdout_key["NSTEP"] = "NSTEP" + stdout_key["ENERGY"] = "ENERGY" # Turn off the header flag now that the data has been recorded. self._is_header = False - # All other protocols have output that is formatted as RECORD = VALUE. + # All other records are formatted as RECORD = VALUE. # Use a regex search to split the line into record names and values. records = _re.findall( - r"(\d*\-*\d*\s*[A-Z]+\(*[A-Z]*\)*)\s*=\s*(\-*\d+\.?\d*)", + r"([SC_]*[EEL_]*[RES_]*[VDW_]*\d*\-*\d*\s*[A-Z/]+\(*[A-Z]*\)*)\s*=\s*(\-*\d+\.?\d*|\**)", line.upper(), ) # Append each record to the dictionary. for key, value in records: - # Strip whitespace from the record key. + # Strip whitespace from beginning and end. key = key.strip() - self._stdout_dict[key] = value + + # Format key so it can be re-used for records corresponding to + # different regions, which use different abbreviations. + universal_key = ( + key.replace("SC_", "") + .replace(" ", "") + .replace("-", "") + .replace("EELEC", "EEL") + .replace("VDWAALS", "VDW") + ) + + # Handle missing values, which will appear as asterisks, e.g. + # PRESS=******** + try: + tmp = float(value) + except: + value = None + + # Store the record using the original key. + stdout_dict[key] = value + + # Map the universal key to the original. + stdout_key[universal_key] = key # Get the current number of lines. num_lines = len(self._stdout) @@ -1680,7 +2671,9 @@ def kill(self): if not self._process is None and self._process.isRunning(): self._process.kill() - def _get_stdout_record(self, key, time_series=False, unit=None): + def _get_stdout_record( + self, key, time_series=False, unit=None, region=0, soft_core=False + ): """ Helper function to get a stdout record from the dictionary. @@ -1688,7 +2681,7 @@ def _get_stdout_record(self, key, time_series=False, unit=None): ---------- key : str - The record key. + The universal record key. time_series : bool Whether to return a time series of records. @@ -1696,6 +2689,15 @@ def _get_stdout_record(self, key, time_series=False, unit=None): unit : :class:`Type ` The unit to convert the record to. + region : int + The region to which the record corresponds. There will only be more + than one region for FreeEnergy protocols, where 1 indicates the second + TI region. + + soft_core : bool + Whether to get the record for the soft-core part of the system for the + chosen region. + Returns ------- @@ -1719,18 +2721,41 @@ def _get_stdout_record(self, key, time_series=False, unit=None): if not isinstance(unit, _Type): raise TypeError("'unit' must be of type 'BioSimSpace.Types'") + # Validate the region. + if not isinstance(region, int): + raise TypeError("'region' must be of type 'int'") + else: + if region < 0 or region > 1: + raise ValueError("'region' must be in range [0, 1]") + + # Validate the soft-core flag. + if not isinstance(soft_core, bool): + raise TypeError("'soft_core' must be of type 'bool'.") + + # Convert to the full index, region + soft_core. + idx = 2 * region + int(soft_core) + + # Extract the dictionary of stdout records for the specified region and soft-core flag. + stdout_dict = self._stdout_dict[idx] + + # Map the universal key to the original key used for this region. + try: + key = self._stdout_key[idx][key] + except: + return None + # Return the list of dictionary values. if time_series: try: if key == "NSTEP": - return [int(x) for x in self._stdout_dict[key]] + return [int(x) for x in stdout_dict[key]] else: if unit is None: - return [float(x) for x in self._stdout_dict[key]] + return [float(x) if x else None for x in stdout_dict[key]] else: return [ - (float(x) * unit)._to_default_unit() - for x in self._stdout_dict[key] + (float(x) * unit)._to_default_unit() if x else None + for x in stdout_dict[key] ] except KeyError: @@ -1740,14 +2765,107 @@ def _get_stdout_record(self, key, time_series=False, unit=None): else: try: if key == "NSTEP": - return int(self._stdout_dict[key][-1]) + return int(stdout_dict[key][-1]) else: if unit is None: - return float(self._stdout_dict[key][-1]) + try: + return float(stdout_dict[key][-1]) + except: + return None else: - return ( - float(self._stdout_dict[key][-1]) * unit - )._to_default_unit() + try: + return ( + float(stdout_dict[key][-1]) * unit + )._to_default_unit() + except: + return None except KeyError: return None + + +def _find_exe(is_gpu=False, is_free_energy=False, is_vacuum=False): + """ + Helper function to search for an AMBER executable. + + Parameters + ---------- + + is_gpu : bool + Whether to search for a GPU-enabled executable. + + is_free_energy : bool + Whether this is a free energy simulation. + + is_vacuum : bool + Whether this is a vacuum simulation. + + Returns + ------- + + exe : str + The path to the executable. + """ + + if not isinstance(is_gpu, bool): + raise TypeError("'is_gpu' must be of type 'bool'.") + + if not isinstance(is_free_energy, bool): + raise TypeError("'is_free_energy' must be of type 'bool'.") + + if not isinstance(is_vacuum, bool): + raise TypeError("'is_vacuum' must be of type 'bool'.") + + if is_gpu: + targets = ["pmemd.cuda"] + else: + if is_free_energy: + targets = ["pmemd"] + else: + targets = ["pmemd", "sander"] + + # Search for the executable. + + import os as _os + import pathlib as _pathlib + + from glob import glob as _glob + + # Get the current path. + path = _os.environ["PATH"].split(_os.pathsep) + + # If AMBERHOME is set, then prepend to the path. + if _amber_home is not None: + path = [_amber_home + "/bin"] + path + + # Helper function to check whether a file is executable. + def is_exe(fpath): + return _os.path.isfile(fpath) and _os.access(fpath, _os.X_OK) + + # Loop over each directory in the path and search for the executable. + for p in path: + # Loop over each target. + for t in targets: + # Glob for the executable. + results = _glob(f"{t}*", root_dir=p) + # If we find a match, check that it's executable and return the path. + # Note that this returns the first match, not the best match. If a + # user requires a specific version of the executable, they should + # order their path accordingly, or use the exe keyword argument. + if results: + for exe in results: + exe = _pathlib.Path(p) / exe + if is_exe(exe): + return str(exe) + + msg = ( + "'BioSimSpace.Process.Amber' is not supported. " + "Unable to find AMBER executable in AMBERHOME or PATH. " + "Please install AMBER (http://ambermd.org)." + ) + + if is_free_energy: + msg += " Free energy simulations require 'pmemd' or 'pmemd.cuda'." + + # If we don't find the executable, raise an error. + raise _MissingSoftwareError(msg) diff --git a/python/BioSimSpace/Process/_gromacs.py b/python/BioSimSpace/Process/_gromacs.py index 166910e05..a35fc3531 100644 --- a/python/BioSimSpace/Process/_gromacs.py +++ b/python/BioSimSpace/Process/_gromacs.py @@ -76,16 +76,19 @@ def __init__( self, system, protocol, + reference_system=None, exe=None, name="gromacs", work_dir=None, seed=None, extra_options={}, extra_lines=[], + extra_args={}, property_map={}, ignore_warnings=False, show_errors=True, checkpoint_file=None, + **kwargs, ): """ Constructor. @@ -99,6 +102,11 @@ def __init__( protocol : :class:`Protocol ` The protocol for the GROMACS process. + reference_system : :class:`System ` or None + An optional system to use as a source of reference coordinates for position + restraints. It is assumed that this system has the same topology as "system". + If this is None, then "system" is used as a reference. + exe : str The full path to the GROMACS executable. @@ -118,6 +126,10 @@ def __init__( extra_lines : [str] A list of extra lines to put at the end of the configuration file. + extra_args : dict + A dictionary of extra command-line arguments to pass to the GROMACS + executable. + property_map : dict A dictionary that maps system "properties" to their user defined values. This allows the user to refer to properties with their @@ -136,17 +148,22 @@ def __init__( The path to a checkpoint file from a previous run. This can be used to continue an existing simulation. Currently we only support the use of checkpoint files for Equilibration protocols. + + kwargs : dict + Additional keyword arguments. """ # Call the base class constructor. super().__init__( system, protocol, + reference_system=reference_system, name=name, work_dir=work_dir, seed=seed, extra_options=extra_options, extra_lines=extra_lines, + extra_args=extra_args, property_map=property_map, ) @@ -193,6 +210,7 @@ def __init__( # The names of the input files. self._gro_file = "%s/%s.gro" % (self._work_dir, name) self._top_file = "%s/%s.top" % (self._work_dir, name) + self._ref_file = "%s/%s_ref.gro" % (self._work_dir, name) # The name of the trajectory file. self._traj_file = "%s/%s.trr" % (self._work_dir, name) @@ -206,6 +224,10 @@ def __init__( # Create the list of input files. self._input_files = [self._config_file, self._gro_file, self._top_file] + # Add the reference file if there are position restraints. + if self._protocol.getRestraint() is not None: + self._input_files.append(self._ref_file) + # Initialise the PLUMED interface object. self._plumed = None @@ -223,9 +245,9 @@ def __init__( ) # Now set up the working directory for the process. - self._setup() + self._setup(**kwargs) - def _setup(self): + def _setup(self, **kwargs): """Setup the input files and working directory ready for simulation.""" # Create the input files... @@ -250,12 +272,24 @@ def _setup(self): ) raise NotImplementedError(msg) + # Apply SOMD1 compatibility to the perturbation. + if ( + "somd1_compatibility" in kwargs + and kwargs.get("somd1_compatibility") is True + ): + from ._somd import _somd1_compatibility + + system = _somd1_compatibility(system) + else: # Check for perturbable molecules and convert to the chosen end state. system = self._checkPerturbable(system) # Convert the water model topology so that it matches the GROMACS naming convention. system._set_water_topology("GROMACS", property_map=self._property_map) + self._reference_system._set_water_topology( + "GROMACS", property_map=self._property_map + ) # GRO87 file. file = _os.path.splitext(self._gro_file)[0] @@ -263,6 +297,16 @@ def _setup(self): file, system, "gro87", match_water=False, property_map=self._property_map ) + # Reference file. + file = _os.path.splitext(self._ref_file)[0] + _IO.saveMolecules( + file, + self._reference_system, + "gro87", + match_water=False, + property_map=self._property_map, + ) + # TOP file. file = _os.path.splitext(self._top_file)[0] _IO.saveMolecules( @@ -422,6 +466,10 @@ def _generate_args(self): if isinstance(self._protocol, (_Protocol.Metadynamics, _Protocol.Steering)): self.setArg("-plumed", "plumed.dat") + # Add any extra arguments. + for key, value in self._extra_args.items(): + self.setArg(key, value) + @staticmethod def _generate_binary_run_file( mdp_file, @@ -433,6 +481,7 @@ def _generate_binary_run_file( checkpoint_file=None, ignore_warnings=False, show_errors=True, + **kwargs, ): """ Use grommp to generate the binary run input file. @@ -472,6 +521,9 @@ def _generate_binary_run_file( show_errors : bool Whether to show warning/error messages when generating the binary run file. + + **kwargs : dict + Additional keyword arguments. """ if not isinstance(mdp_file, str): @@ -1992,8 +2044,8 @@ def _add_position_restraints(self): property_map["parallel"] = _SireBase.wrap(False) property_map["sort"] = _SireBase.wrap(False) - # Create a copy of the system. - system = self._system.copy() + # Create a copy of the reference system. + system = self._reference_system.copy() # Convert to the lambda = 0 state if this is a perturbable system and this # isn't a free energy protocol. diff --git a/python/BioSimSpace/Process/_namd.py b/python/BioSimSpace/Process/_namd.py index 25ecaa5f3..9811d26ab 100644 --- a/python/BioSimSpace/Process/_namd.py +++ b/python/BioSimSpace/Process/_namd.py @@ -63,11 +63,13 @@ def __init__( self, system, protocol, + reference_system=None, exe=None, name="namd", work_dir=None, seed=None, property_map={}, + **kwargs, ): """ Constructor. @@ -81,6 +83,11 @@ def __init__( protocol : :class:`Protocol ` The protocol for the NAMD process. + reference_system : :class:`System ` or None + An optional system to use as a source of reference coordinates for position + restraints. It is assumed that this system has the same topology as "system". + If this is None, then "system" is used as a reference. + exe : str The full path to the NAMD executable. @@ -97,12 +104,16 @@ def __init__( A dictionary that maps system "properties" to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { "charge" : "my-charge" } + + kwargs : dict + Additional keyword arguments. """ # Call the base class constructor. super().__init__( system, protocol, + reference_system=reference_system, name=name, work_dir=work_dir, seed=seed, @@ -421,7 +432,9 @@ def _generate_config(self): restraint = self._protocol.getRestraint() if restraint is not None: # Create a restrained system. - restrained = self._createRestrainedSystem(self._system, restraint) + restrained = self._createRestrainedSystem( + self._reference_system, restraint + ) # Create a PDB object, mapping the "occupancy" property to "restrained". prop = self._property_map.get("occupancy", "occupancy") @@ -761,9 +774,7 @@ def getSystem(self, block="AUTO"): is_lambda1 = False # Load the restart file. - new_system = _System( - _SireIO.MoleculeParser.read(files, self._property_map) - ) + new_system = _IO.readMolecules(files, property_map=self._property_map) # Create a copy of the existing system object. old_system = self._system.copy() diff --git a/python/BioSimSpace/Process/_openmm.py b/python/BioSimSpace/Process/_openmm.py index 557bef80e..d11974d22 100644 --- a/python/BioSimSpace/Process/_openmm.py +++ b/python/BioSimSpace/Process/_openmm.py @@ -72,12 +72,14 @@ def __init__( self, system, protocol, + reference_system=None, exe=None, name="openmm", platform="CPU", work_dir=None, seed=None, property_map={}, + **kwargs, ): """ Constructor. @@ -91,6 +93,11 @@ def __init__( protocol : :class:`Protocol ` The protocol for the OpenMM process. + reference_system : :class:`System ` or None + An optional system to use as a source of reference coordinates for position + restraints. It is assumed that this system has the same topology as "system". + If this is None, then "system" is used as a reference. + exe : str The full path to the Python interpreter used to run OpenMM. @@ -114,12 +121,16 @@ def __init__( A dictionary that maps system "properties" to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { "charge" : "my-charge" } + + kwargs : dict + Additional keyword arguments. """ # Call the base class constructor. super().__init__( system, protocol, + reference_system=reference_system, name=name, work_dir=work_dir, seed=seed, @@ -175,6 +186,7 @@ def __init__( # are self-contained, but could equally work with GROMACS files. self._rst_file = "%s/%s.rst7" % (self._work_dir, name) self._top_file = "%s/%s.prm7" % (self._work_dir, name) + self._ref_file = "%s/%s_ref.rst7" % (self._work_dir, name) # The name of the trajectory file. self._traj_file = "%s/%s.dcd" % (self._work_dir, name) @@ -186,6 +198,10 @@ def __init__( # Create the list of input files. self._input_files = [self._config_file, self._rst_file, self._top_file] + # Add the reference file if there are position restraints. + if self._protocol.getRestraint() is not None: + self._input_files.append(self._ref_file) + # Initialise the log file header. self._header = None @@ -232,6 +248,9 @@ def _setup(self): # Convert the water model topology so that it matches the AMBER naming convention. system._set_water_topology("AMBER", property_map=self._property_map) + self._reference_system._set_water_topology( + "AMBER", property_map=self._property_map + ) # Check for perturbable molecules and convert to the chosen end state. system = self._checkPerturbable(system) @@ -249,6 +268,23 @@ def _setup(self): else: raise IOError(msg) from None + # Reference coordinate file for position restraints. + if self._protocol.getRestraint() is not None: + try: + file = _os.path.splitext(self._ref_file)[0] + _IO.saveMolecules( + file, + self._reference_system, + "rst7", + property_map=self._property_map, + ) + except Exception as e: + msg = "Failed to write reference system to 'RST7' format." + if _isVerbose(): + raise IOError(msg) from e + else: + raise IOError(msg) from None + # PRM file (topology). try: file = _os.path.splitext(self._top_file)[0] @@ -2140,11 +2176,15 @@ def _add_config_restraints(self): if restraint is not None: # Search for the atoms to restrain by keyword. if isinstance(restraint, str): - restrained_atoms = self._system.getRestraintAtoms(restraint) + restrained_atoms = self._reference_system.getRestraintAtoms(restraint) # Use the user-defined list of indices. else: restrained_atoms = restraint + self.addToConfig( + f"ref_prm = parmed.load_file('{self._name}.prm7', '{self._name}_ref.rst7')" + ) + # Get the force constant in units of kJ_per_mol/nanometer**2 force_constant = self._protocol.getForceConstant()._sire_unit force_constant = force_constant.to( @@ -2161,7 +2201,7 @@ def _add_config_restraints(self): "nonbonded = [f for f in system.getForces() if isinstance(f, NonbondedForce)][0]" ) self.addToConfig("dummy_indices = []") - self.addToConfig("positions = prm.positions") + self.addToConfig("positions = ref_prm.positions") self.addToConfig(f"restrained_atoms = {restrained_atoms}") self.addToConfig("for i in restrained_atoms:") self.addToConfig(" j = system.addParticle(0)") diff --git a/python/BioSimSpace/Process/_process.py b/python/BioSimSpace/Process/_process.py index 255dee9df..a4ef0ebf2 100644 --- a/python/BioSimSpace/Process/_process.py +++ b/python/BioSimSpace/Process/_process.py @@ -70,11 +70,13 @@ def __init__( self, system, protocol, + reference_system=None, name=None, work_dir=None, seed=None, extra_options={}, extra_lines=[], + extra_args={}, property_map={}, ): """ @@ -89,6 +91,11 @@ def __init__( protocol : :class:`Protocol ` The protocol for the process. + reference_system : :class:`System ` or None + An optional system to use as a source of reference coordinates for position + restraints. It is assumed that this system has the same topology as "system". + If this is None, then "system" is used as a reference. + name : str The name of the process. @@ -109,6 +116,9 @@ def __init__( extra_lines : [str] A list of extra lines to put at the end of the configuration file. + extra_args : dict + A dictionary containing extra command-line arguments. + property_map : dict A dictionary that maps system "properties" to their user defined values. This allows the user to refer to properties with their @@ -137,6 +147,27 @@ def __init__( if not isinstance(protocol, _Protocol): raise TypeError("'protocol' must be of type 'BioSimSpace.Protocol'") + # Check that the reference system is valid. + if reference_system is not None: + if not isinstance(reference_system, _System): + raise TypeError( + "'reference_system' must be of type 'BioSimSpace._SireWrappers.System'" + ) + + # Make sure that the reference system contains the same number + # of molecules, residues, and atoms as the system. + if ( + not reference_system.nMolecules() == system.nMolecules() + or not reference_system.nResidues() == system.nResidues() + or not reference_system.nAtoms() == system.nAtoms() + ): + raise _IncompatibleError( + "'refence_system' must have the same topology as 'system'" + ) + self._reference_system = reference_system + else: + self._reference_system = system.copy() + # Check that the working directory is valid. if work_dir is not None and not isinstance(work_dir, (str, _Utils.WorkDir)): raise TypeError( @@ -162,6 +193,14 @@ def __init__( if not all(isinstance(line, str) for line in extra_lines): raise TypeError("Lines in 'extra_lines' must be of type 'str'.") + # Check the extra arguments. + if not isinstance(extra_args, dict): + raise TypeError("'extra_args' must be of type 'dict'.") + else: + keys = extra_args.keys() + if not all(isinstance(k, str) for k in keys): + raise TypeError("Keys of 'extra_args' must be of type 'str'.") + # Check that the map is valid. if not isinstance(property_map, dict): raise TypeError("'property_map' must be of type 'dict'") @@ -217,9 +256,10 @@ def __init__( self._is_seeded = True self.setSeed(seed) - # Set the extra options and lines. + # Set the extra options, lines, and args. self._extra_options = extra_options self._extra_lines = extra_lines + self._extra_args = extra_args # Set the map. self._property_map = property_map.copy() @@ -1434,6 +1474,10 @@ def setArgs(self, args): "'args' must be of type 'dict' or 'collections.OrderedDict'" ) + # Add extra arguments. + if self._extra_args: + self.addArgs(self._extra_args) + def setArg(self, arg, value): """ Set a specific command-line argument. diff --git a/python/BioSimSpace/Process/_somd.py b/python/BioSimSpace/Process/_somd.py index 885afa398..1f3094daf 100644 --- a/python/BioSimSpace/Process/_somd.py +++ b/python/BioSimSpace/Process/_somd.py @@ -79,6 +79,7 @@ def __init__( extra_options={}, extra_lines=[], property_map={}, + **kwargs, ): """ Constructor. @@ -121,6 +122,9 @@ def __init__( A dictionary that maps system "properties" to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { "charge" : "my-charge" } + + kwargs : dict + Additional keyword arguments. """ # Call the base class constructor. @@ -3043,3 +3047,504 @@ def _random_suffix(basename, size=4, chars=_string.ascii_uppercase + _string.dig + "AMBER atom names can only be 4 characters wide." ) return "".join(_random.choice(chars) for _ in range(size - basename_size)) + + +def _somd1_compatibility(system): + """ + Makes a perturbation SOMD1 compatible. + + Parameters + ---------- + + system : :class:`System ` + The system containing the molecules to be perturbed. + + Returns + ------- + + system : :class:`System ` + The updated system. + """ + + # Check the system is a Sire system. + if not isinstance(system, _System): + raise TypeError("'system' must of type 'BioSimSpace._SireWrappers.System'") + + # Search for perturbable molecules. + pert_mols = system.getPerturbableMolecules() + if len(pert_mols) == 0: + raise KeyError("No perturbable molecules in the system") + + # Store a dummy element. + dummy = _SireMol.Element("Xx") + + for mol in pert_mols: + # Get the underlying Sire molecule. + mol = mol._sire_object + + # Store the molecule info. + info = mol.info() + + # Get an editable version of the molecule. + edit_mol = mol.edit() + + ########################## + # First process the bonds. + ########################## + + new_bonds0 = _SireMM.TwoAtomFunctions(mol.info()) + new_bonds1 = _SireMM.TwoAtomFunctions(mol.info()) + + # Extract the bonds at lambda = 0 and 1. + bonds0 = mol.property("bond0").potentials() + bonds1 = mol.property("bond1").potentials() + + # Dictionaries to store the BondIDs at lambda = 0 and 1. + bonds0_idx = {} + bonds1_idx = {} + + # Loop over all bonds at lambda = 0. + for idx, bond in enumerate(bonds0): + # Get the AtomIdx for the atoms in the bond. + idx0 = info.atom_idx(bond.atom0()) + idx1 = info.atom_idx(bond.atom1()) + + # Create the BondID. + bond_id = _SireMol.BondID(idx0, idx1) + + # Add to the list of ids. + bonds0_idx[bond_id] = idx + + # Loop over all bonds at lambda = 1. + for idx, bond in enumerate(bonds1): + # Get the AtomIdx for the atoms in the bond. + idx0 = info.atom_idx(bond.atom0()) + idx1 = info.atom_idx(bond.atom1()) + + # Create the BondID. + bond_id = _SireMol.BondID(idx0, idx1) + + # Add to the list of ids. + if bond_id.mirror() in bonds0_idx: + bonds1_idx[bond_id.mirror()] = idx + else: + bonds1_idx[bond_id] = idx + + # Now work out the BondIDs that are unique at lambda = 0 and 1 + # as well as those that are shared. + bonds0_unique_idx = {} + bonds1_unique_idx = {} + bonds_shared_idx = {} + + # lambda = 0. + for idx in bonds0_idx.keys(): + if idx not in bonds1_idx.keys(): + bonds0_unique_idx[idx] = bonds0_idx[idx] + else: + bonds_shared_idx[idx] = (bonds0_idx[idx], bonds1_idx[idx]) + + # lambda = 1. + for idx in bonds1_idx.keys(): + if idx not in bonds0_idx.keys(): + bonds1_unique_idx[idx] = bonds1_idx[idx] + elif idx not in bonds_shared_idx.keys(): + bonds_shared_idx[idx] = (bonds0_idx[idx], bonds1_idx[idx]) + + # Loop over the shared bonds. + for idx0, idx1 in bonds_shared_idx.values(): + # Get the bond potentials. + p0 = bonds0[idx0] + p1 = bonds1[idx1] + + # Get the AtomIdx for the atoms in the angle. + idx0 = p0.atom0() + idx1 = p0.atom1() + + # Check whether a dummy atoms are present in the lambda = 0 + # and lambda = 1 states. + initial_dummy = _has_dummy(mol, [idx0, idx1]) + final_dummy = _has_dummy(mol, [idx0, idx1], True) + + # If there is a dummy, then set the potential to the opposite state. + # This should already be the case, but we explicitly set it here. + + if initial_dummy: + new_bonds0.set(idx0, idx1, p1.function()) + new_bonds1.set(idx0, idx1, p1.function()) + elif final_dummy: + new_bonds0.set(idx0, idx1, p0.function()) + new_bonds1.set(idx0, idx1, p0.function()) + else: + new_bonds0.set(idx0, idx1, p0.function()) + new_bonds1.set(idx0, idx1, p1.function()) + + # Set the new bonded terms. + edit_mol = edit_mol.set_property("bond0", new_bonds0).molecule() + edit_mol = edit_mol.set_property("bond1", new_bonds1).molecule() + + ######################### + # Now process the angles. + ######################### + + new_angles0 = _SireMM.ThreeAtomFunctions(mol.info()) + new_angles1 = _SireMM.ThreeAtomFunctions(mol.info()) + + # Extract the angles at lambda = 0 and 1. + angles0 = mol.property("angle0").potentials() + angles1 = mol.property("angle1").potentials() + + # Dictionaries to store the AngleIDs at lambda = 0 and 1. + angles0_idx = {} + angles1_idx = {} + + # Loop over all angles at lambda = 0. + for idx, angle in enumerate(angles0): + # Get the AtomIdx for the atoms in the angle. + idx0 = info.atom_idx(angle.atom0()) + idx1 = info.atom_idx(angle.atom1()) + idx2 = info.atom_idx(angle.atom2()) + + # Create the AngleID. + angle_id = _SireMol.AngleID(idx0, idx1, idx2) + + # Add to the list of ids. + angles0_idx[angle_id] = idx + + # Loop over all angles at lambda = 1. + for idx, angle in enumerate(angles1): + # Get the AtomIdx for the atoms in the angle. + idx0 = info.atom_idx(angle.atom0()) + idx1 = info.atom_idx(angle.atom1()) + idx2 = info.atom_idx(angle.atom2()) + + # Create the AngleID. + angle_id = _SireMol.AngleID(idx0, idx1, idx2) + + # Add to the list of ids. + if angle_id.mirror() in angles0_idx: + angles1_idx[angle_id.mirror()] = idx + else: + angles1_idx[angle_id] = idx + + # Now work out the AngleIDs that are unique at lambda = 0 and 1 + # as well as those that are shared. + angles0_unique_idx = {} + angles1_unique_idx = {} + angles_shared_idx = {} + + # lambda = 0. + for idx in angles0_idx.keys(): + if idx not in angles1_idx.keys(): + angles0_unique_idx[idx] = angles0_idx[idx] + else: + angles_shared_idx[idx] = (angles0_idx[idx], angles1_idx[idx]) + + # lambda = 1. + for idx in angles1_idx.keys(): + if idx not in angles0_idx.keys(): + angles1_unique_idx[idx] = angles1_idx[idx] + elif idx not in angles_shared_idx.keys(): + angles_shared_idx[idx] = (angles0_idx[idx], angles1_idx[idx]) + + # Loop over the angles. + for idx0, idx1 in angles_shared_idx.values(): + # Get the angle potentials. + p0 = angles0[idx0] + p1 = angles1[idx1] + + # Get the AtomIdx for the atoms in the angle. + idx0 = p0.atom0() + idx1 = p0.atom1() + idx2 = p0.atom2() + + # Check whether a dummy atoms are present in the lambda = 0 + # and lambda = 1 states. + initial_dummy = _has_dummy(mol, [idx0, idx1, idx2]) + final_dummy = _has_dummy(mol, [idx0, idx1, idx2], True) + + # If both end states contain a dummy, the use null potentials. + if initial_dummy and final_dummy: + theta = _SireCAS.Symbol("theta") + null_angle = _SireMM.AmberAngle(0.0, theta).to_expression(theta) + new_angles0.set(idx0, idx1, idx2, null_angle) + new_angles1.set(idx0, idx1, idx2, null_angle) + # If the initial state contains a dummy, then use the potential from the final state. + # This should already be the case, but we explicitly set it here. + elif initial_dummy: + new_angles0.set(idx0, idx1, idx2, p1.function()) + new_angles1.set(idx0, idx1, idx2, p1.function()) + # If the final state contains a dummy, then use the potential from the initial state. + # This should already be the case, but we explicitly set it here. + elif final_dummy: + new_angles0.set(idx0, idx1, idx2, p0.function()) + new_angles1.set(idx0, idx1, idx2, p0.function()) + # Otherwise, use the potentials from the initial and final states. + else: + new_angles0.set(idx0, idx1, idx2, p0.function()) + new_angles1.set(idx0, idx1, idx2, p1.function()) + + # Set the new angle terms. + edit_mol = edit_mol.set_property("angle0", new_angles0).molecule() + edit_mol = edit_mol.set_property("angle1", new_angles1).molecule() + + ############################ + # Now process the dihedrals. + ############################ + + new_dihedrals0 = _SireMM.FourAtomFunctions(mol.info()) + new_dihedrals1 = _SireMM.FourAtomFunctions(mol.info()) + + # Extract the dihedrals at lambda = 0 and 1. + dihedrals0 = mol.property("dihedral0").potentials() + dihedrals1 = mol.property("dihedral1").potentials() + + # Dictionaries to store the DihedralIDs at lambda = 0 and 1. + dihedrals0_idx = {} + dihedrals1_idx = {} + + # Loop over all dihedrals at lambda = 0. + for idx, dihedral in enumerate(dihedrals0): + # Get the AtomIdx for the atoms in the dihedral. + idx0 = info.atom_idx(dihedral.atom0()) + idx1 = info.atom_idx(dihedral.atom1()) + idx2 = info.atom_idx(dihedral.atom2()) + idx3 = info.atom_idx(dihedral.atom3()) + + # Create the DihedralID. + dihedral_id = _SireMol.DihedralID(idx0, idx1, idx2, idx3) + + # Add to the list of ids. + dihedrals0_idx[dihedral_id] = idx + + # Loop over all dihedrals at lambda = 1. + for idx, dihedral in enumerate(dihedrals1): + # Get the AtomIdx for the atoms in the dihedral. + idx0 = info.atom_idx(dihedral.atom0()) + idx1 = info.atom_idx(dihedral.atom1()) + idx2 = info.atom_idx(dihedral.atom2()) + idx3 = info.atom_idx(dihedral.atom3()) + + # Create the DihedralID. + dihedral_id = _SireMol.DihedralID(idx0, idx1, idx2, idx3) + + # Add to the list of ids. + if dihedral_id.mirror() in dihedrals0_idx: + dihedrals1_idx[dihedral_id.mirror()] = idx + else: + dihedrals1_idx[dihedral_id] = idx + + # Now work out the DihedralIDs that are unique at lambda = 0 and 1 + # as well as those that are shared. + dihedrals0_unique_idx = {} + dihedrals1_unique_idx = {} + dihedrals_shared_idx = {} + + # lambda = 0. + for idx in dihedrals0_idx.keys(): + if idx not in dihedrals1_idx.keys(): + dihedrals0_unique_idx[idx] = dihedrals0_idx[idx] + else: + dihedrals_shared_idx[idx] = (dihedrals0_idx[idx], dihedrals1_idx[idx]) + + # lambda = 1. + for idx in dihedrals1_idx.keys(): + if idx not in dihedrals0_idx.keys(): + dihedrals1_unique_idx[idx] = dihedrals1_idx[idx] + elif idx not in dihedrals_shared_idx.keys(): + dihedrals_shared_idx[idx] = (dihedrals0_idx[idx], dihedrals1_idx[idx]) + + # Loop over the dihedrals. + for idx0, idx1 in dihedrals_shared_idx.values(): + # Get the dihedral potentials. + p0 = dihedrals0[idx0] + p1 = dihedrals1[idx1] + + # Get the AtomIdx for the atoms in the dihedral. + idx0 = info.atom_idx(p0.atom0()) + idx1 = info.atom_idx(p0.atom1()) + idx2 = info.atom_idx(p0.atom2()) + idx3 = info.atom_idx(p0.atom3()) + + # Whether any atom in each end state is a dummy. + has_dummy_initial = _has_dummy(mol, [idx0, idx1, idx2, idx3]) + has_dummy_final = _has_dummy(mol, [idx0, idx1, idx2, idx3], True) + + # Whether all atoms in each state are dummies. + all_dummy_initial = all(_is_dummy(mol, [idx0, idx1, idx2, idx3])) + all_dummy_final = all(_is_dummy(mol, [idx0, idx1, idx2, idx3], True)) + + # If both end states contain a dummy, the use null potentials. + if has_dummy_initial and has_dummy_final: + phi = _SireCAS.Symbol("phi") + null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi) + new_dihedrals0.set(idx0, idx1, idx2, idx3, null_dihedral) + new_dihedrals1.set(idx0, idx1, idx2, idx3, null_dihedral) + elif has_dummy_initial: + # If all the atoms are dummy, then use the potential from the final state. + if all_dummy_initial: + new_dihedrals0.set(idx0, idx1, idx2, idx3, p1.function()) + new_dihedrals1.set(idx0, idx1, idx2, idx3, p1.function()) + # Otherwise, zero the potential. + else: + phi = _SireCAS.Symbol("phi") + null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi) + new_dihedrals0.set(idx0, idx1, idx2, idx3, null_dihedral) + new_dihedrals1.set(idx0, idx1, idx2, idx3, p1.function()) + elif has_dummy_final: + # If all the atoms are dummy, then use the potential from the initial state. + if all_dummy_final: + new_dihedrals0.set(idx0, idx1, idx2, idx3, p0.function()) + new_dihedrals1.set(idx0, idx1, idx2, idx3, p0.function()) + # Otherwise, zero the potential. + else: + phi = _SireCAS.Symbol("phi") + null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi) + new_dihedrals0.set(idx0, idx1, idx2, idx3, p0.function()) + new_dihedrals1.set(idx0, idx1, idx2, idx3, null_dihedral) + else: + new_dihedrals0.set(idx0, idx1, idx2, idx3, p0.function()) + new_dihedrals1.set(idx0, idx1, idx2, idx3, p1.function()) + + # Set the new dihedral terms. + edit_mol = edit_mol.set_property("dihedral0", new_dihedrals0).molecule() + edit_mol = edit_mol.set_property("dihedral1", new_dihedrals1).molecule() + + ############################ + # Now process the impropers. + ############################ + + new_impropers0 = _SireMM.FourAtomFunctions(mol.info()) + new_impropers1 = _SireMM.FourAtomFunctions(mol.info()) + + # Extract the impropers at lambda = 0 and 1. + impropers0 = mol.property("improper0").potentials() + impropers1 = mol.property("improper1").potentials() + + # Dictionaries to store the ImproperIDs at lambda = 0 and 1. + impropers0_idx = {} + impropers1_idx = {} + + # Loop over all impropers at lambda = 0. + for idx, improper in enumerate(impropers0): + # Get the AtomIdx for the atoms in the improper. + idx0 = info.atom_idx(improper.atom0()) + idx1 = info.atom_idx(improper.atom1()) + idx2 = info.atom_idx(improper.atom2()) + idx3 = info.atom_idx(improper.atom3()) + + # Create the ImproperID. + improper_id = _SireMol.ImproperID(idx0, idx1, idx2, idx3) + + # Add to the list of ids. + impropers0_idx[improper_id] = idx + + # Loop over all impropers at lambda = 1. + for idx, improper in enumerate(impropers1): + # Get the AtomIdx for the atoms in the improper. + idx0 = info.atom_idx(improper.atom0()) + idx1 = info.atom_idx(improper.atom1()) + idx2 = info.atom_idx(improper.atom2()) + idx3 = info.atom_idx(improper.atom3()) + + # Create the ImproperID. + improper_id = _SireMol.ImproperID(idx0, idx1, idx2, idx3) + + # Add to the list of ids. + # You cannot mirror an improper! + impropers1_idx[improper_id] = idx + + # Now work out the ImproperIDs that are unique at lambda = 0 and 1 + # as well as those that are shared. Note that the ordering of + # impropers is inconsistent between molecular topology formats so + # we test all permutations of atom ordering to find matches. This + # is achieved using the ImproperID.equivalent() method. + impropers0_unique_idx = {} + impropers1_unique_idx = {} + impropers_shared_idx = {} + + # lambda = 0. + for idx0 in impropers0_idx.keys(): + for idx1 in impropers1_idx.keys(): + if idx0.equivalent(idx1): + impropers_shared_idx[idx0] = ( + impropers0_idx[idx0], + impropers1_idx[idx1], + ) + break + else: + impropers0_unique_idx[idx0] = impropers0_idx[idx0] + + # lambda = 1. + for idx1 in impropers1_idx.keys(): + for idx0 in impropers0_idx.keys(): + if idx1.equivalent(idx0): + # Don't store duplicates. + if not idx0 in impropers_shared_idx.keys(): + impropers_shared_idx[idx1] = ( + impropers0_idx[idx0], + impropers1_idx[idx1], + ) + break + else: + impropers1_unique_idx[idx1] = impropers1_idx[idx1] + + # Loop over the impropers. + for idx0, idx1 in impropers_shared_idx.values(): + # Get the improper potentials. + p0 = impropers0[idx0] + p1 = impropers1[idx1] + + # Get the AtomIdx for the atoms in the dihedral. + idx0 = info.atom_idx(p0.atom0()) + idx1 = info.atom_idx(p0.atom1()) + idx2 = info.atom_idx(p0.atom2()) + idx3 = info.atom_idx(p0.atom3()) + + # Whether any atom in each end state is a dummy. + has_dummy_initial = _has_dummy(mol, [idx0, idx1, idx2, idx3]) + has_dummy_final = _has_dummy(mol, [idx0, idx1, idx2, idx3], True) + + # Whether all atoms in each state are dummies. + all_dummy_initial = all(_is_dummy(mol, [idx0, idx1, idx2, idx3])) + all_dummy_final = all(_is_dummy(mol, [idx0, idx1, idx2, idx3], True)) + + if has_dummy_initial and has_dummy_final: + phi = _SireCAS.Symbol("phi") + null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi) + new_impropers0.set(idx0, idx1, idx2, idx3, null_dihedral) + new_impropers1.set(idx0, idx1, idx2, idx3, null_dihedral) + elif has_dummy_initial: + # If all the atoms are dummy, then use the potential from the final state. + if all_dummy_initial: + new_impropers0.set(idx0, idx1, idx2, idx3, p1.function()) + new_impropers1.set(idx0, idx1, idx2, idx3, p1.function()) + # Otherwise, zero the potential. + else: + phi = _SireCAS.Symbol("phi") + null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi) + new_impropers0.set(idx0, idx1, idx2, idx3, null_dihedral) + new_impropers1.set(idx0, idx1, idx2, idx3, p1.function()) + elif has_dummy_final: + # If all the atoms are dummy, then use the potential from the initial state. + if all_dummy_final: + new_impropers0.set(idx0, idx1, idx2, idx3, p0.function()) + new_impropers1.set(idx0, idx1, idx2, idx3, p0.function()) + # Otherwise, zero the potential. + else: + phi = _SireCAS.Symbol("phi") + null_dihedral = _SireMM.AmberDihedral(0.0, phi).to_expression(phi) + new_impropers0.set(idx0, idx1, idx2, idx3, p0.function()) + new_impropers1.set(idx0, idx1, idx2, idx3, null_dihedral) + else: + new_impropers0.set(idx0, idx1, idx2, idx3, p0.function()) + new_impropers1.set(idx0, idx1, idx2, idx3, p1.function()) + + # Set the new improper terms. + edit_mol = edit_mol.set_property("improper0", new_impropers0).molecule() + edit_mol = edit_mol.set_property("improper1", new_impropers1).molecule() + + # Commit the changes and update the molecule in the system. + system._sire_object.update(edit_mol.commit()) + + # Return the updated system. + return system diff --git a/python/BioSimSpace/Sandpit/Exscientia/Align/_merge.py b/python/BioSimSpace/Sandpit/Exscientia/Align/_merge.py index 859662a16..29dbf731f 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/Align/_merge.py +++ b/python/BioSimSpace/Sandpit/Exscientia/Align/_merge.py @@ -1561,6 +1561,12 @@ def _removeDummies(molecule, is_lambda1): is_lambda1=is_lambda1, generate_intrascale=True ) + # Remove the parameters property, if it exists. + if "parameters" in molecule._sire_object.propertyKeys(): + molecule._sire_object = ( + molecule._sire_object.edit().removeProperty("parameters").commit() + ) + # Set the coordinates to those at lambda = 0 molecule._sire_object = ( molecule._sire_object.edit().setProperty("coordinates", coordinates).commit() diff --git a/python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint_search.py b/python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint_search.py index f7ec62dd4..31a53e956 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint_search.py +++ b/python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint_search.py @@ -2145,9 +2145,9 @@ def _getRestraintDict(u, pairs_ordered): } # If this is the first pair, add it as the permanent distance restraint. if i == 0: - restraint_dict[ - "permanent_distance_restraint" - ] = individual_restraint_dict + restraint_dict["permanent_distance_restraint"] = ( + individual_restraint_dict + ) else: restraint_dict["distance_restraints"].append( individual_restraint_dict diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py index 7c9f66309..257deef09 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py +++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_amber.py @@ -805,23 +805,51 @@ def getFrame(self, index): # Create a copy of the existing system object. old_system = self._system.copy() - # Update the coordinates and velocities and return a mapping between - # the molecule indices in the two systems. - sire_system, mapping = _SireIO.updateCoordinatesAndVelocities( - old_system._sire_object, - new_system._sire_object, - self._mapping, - is_lambda1, - self._property_map, - self._property_map, - ) + if isinstance(self._protocol, _Protocol._FreeEnergyMixin): + # Udpate the coordinates and velocities and return a mapping between + # the molecule indices in the two systems. + mapping = { + _SireMol.MolIdx(x): _SireMol.MolIdx(x) + for x in range(0, self._squashed_system.nMolecules()) + } + ( + self._squashed_system._sire_object, + _, + ) = _SireIO.updateCoordinatesAndVelocities( + self._squashed_system._sire_object, + new_system._sire_object, + mapping, + is_lambda1, + self._property_map, + self._property_map, + ) + + # Update the unsquashed system based on the updated squashed system. + old_system = _unsquash( + old_system, + self._squashed_system, + self._mapping, + explicit_dummies=self._explicit_dummies, + ) + + else: + # Update the coordinates and velocities and return a mapping between + # the molecule indices in the two systems. + sire_system, mapping = _SireIO.updateCoordinatesAndVelocities( + old_system._sire_object, + new_system._sire_object, + self._mapping, + is_lambda1, + self._property_map, + self._property_map, + ) - # Update the underlying Sire object. - old_system._sire_object = sire_system + # Update the underlying Sire object. + old_system._sire_object = sire_system - # Store the mapping between the MolIdx in both systems so we don't - # need to recompute it next time. - self._mapping = mapping + # Store the mapping between the MolIdx in both systems so we don't + # need to recompute it next time. + self._mapping = mapping # Update the box information in the original system. if "space" in new_system._sire_object.propertyKeys(): diff --git a/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py b/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py index 314f31a92..ca02c05b9 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py +++ b/python/BioSimSpace/Sandpit/Exscientia/Process/_namd.py @@ -759,9 +759,7 @@ def getSystem(self, block="AUTO"): is_lambda1 = False # Load the restart file. - new_system = _System( - _SireIO.MoleculeParser.read(files, self._property_map) - ) + new_system = _IO.readMolecules(files, property_map=self._property_map) # Create a copy of the existing system object. old_system = self._system.copy() diff --git a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py index a08935d9b..5b9f53f6f 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py +++ b/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py @@ -217,9 +217,9 @@ def generateAmberConfig(self, extra_options=None, extra_lines=None): protocol_dict["imin"] = 1 # Minimisation simulation. protocol_dict["ntmin"] = 2 # Set the minimisation method to XMIN protocol_dict["maxcyc"] = self._steps # Set the number of steps. - protocol_dict[ - "ncyc" - ] = num_steep # Set the number of steepest descent steps. + protocol_dict["ncyc"] = ( + num_steep # Set the number of steepest descent steps. + ) # FIX need to remove and fix this, only for initial testing timestep = 0.004 else: @@ -318,9 +318,9 @@ def generateAmberConfig(self, extra_options=None, extra_lines=None): # Don't use barostat for vacuum simulations. if self._has_box and self._has_water: protocol_dict["ntp"] = 1 # Isotropic pressure scaling. - protocol_dict[ - "pres0" - ] = f"{self.protocol.getPressure().bar().value():.5f}" # Pressure in bar. + protocol_dict["pres0"] = ( + f"{self.protocol.getPressure().bar().value():.5f}" # Pressure in bar. + ) if isinstance(self.protocol, _Protocol.Equilibration): protocol_dict["barostat"] = 1 # Berendsen barostat. else: @@ -466,23 +466,23 @@ def generateGromacsConfig( protocol_dict["cutoff-scheme"] = "Verlet" # Use Verlet pair lists. if self._has_box and self._has_water: protocol_dict["ns-type"] = "grid" # Use a grid to search for neighbours. - protocol_dict[ - "nstlist" - ] = "20" # Rebuild neighbour list every 20 steps. Recommended in the manual for parallel simulations and/or non-bonded force calculation on the GPU. + protocol_dict["nstlist"] = ( + "20" # Rebuild neighbour list every 20 steps. Recommended in the manual for parallel simulations and/or non-bonded force calculation on the GPU. + ) protocol_dict["rlist"] = "0.8" # Set short-range cutoff. protocol_dict["rvdw"] = "0.8" # Set van der Waals cutoff. protocol_dict["rcoulomb"] = "0.8" # Set Coulomb cutoff. protocol_dict["coulombtype"] = "PME" # Fast smooth Particle-Mesh Ewald. - protocol_dict[ - "DispCorr" - ] = "EnerPres" # Dispersion corrections for energy and pressure. + protocol_dict["DispCorr"] = ( + "EnerPres" # Dispersion corrections for energy and pressure. + ) else: # Perform vacuum simulations by implementing pseudo-PBC conditions, # i.e. run calculation in a near-infinite box (333.3 nm). # c.f.: https://pubmed.ncbi.nlm.nih.gov/29678588 - protocol_dict[ - "nstlist" - ] = "1" # Single neighbour list (all particles interact). + protocol_dict["nstlist"] = ( + "1" # Single neighbour list (all particles interact). + ) protocol_dict["rlist"] = "333.3" # "Infinite" short-range cutoff. protocol_dict["rvdw"] = "333.3" # "Infinite" van der Waals cutoff. protocol_dict["rcoulomb"] = "333.3" # "Infinite" Coulomb cutoff. @@ -503,12 +503,12 @@ def generateGromacsConfig( # 4ps time constant for pressure coupling. # As the tau-p has to be 10 times larger than nstpcouple * dt (4 fs) protocol_dict["tau-p"] = 4 - protocol_dict[ - "ref-p" - ] = f"{self.protocol.getPressure().bar().value():.5f}" # Pressure in bar. - protocol_dict[ - "compressibility" - ] = "4.5e-5" # Compressibility of water. + protocol_dict["ref-p"] = ( + f"{self.protocol.getPressure().bar().value():.5f}" # Pressure in bar. + ) + protocol_dict["compressibility"] = ( + "4.5e-5" # Compressibility of water. + ) else: _warnings.warn( "Cannot use a barostat for a vacuum or non-periodic simulation" @@ -518,9 +518,9 @@ def generateGromacsConfig( if not isinstance(self.protocol, _Protocol.Minimisation): protocol_dict["integrator"] = "md" # leap-frog dynamics. protocol_dict["tcoupl"] = "v-rescale" - protocol_dict[ - "tc-grps" - ] = "system" # A single temperature group for the entire system. + protocol_dict["tc-grps"] = ( + "system" # A single temperature group for the entire system. + ) protocol_dict["tau-t"] = "{:.5f}".format( self.protocol.getTauT().picoseconds().value() ) # Collision frequency (ps). @@ -535,12 +535,12 @@ def generateGromacsConfig( timestep = self.protocol.getTimeStep().picoseconds().value() end_time = _math.floor(timestep * self._steps) - protocol_dict[ - "annealing" - ] = "single" # Single sequence of annealing points. - protocol_dict[ - "annealing-npoints" - ] = 2 # Two annealing points for "system" temperature group. + protocol_dict["annealing"] = ( + "single" # Single sequence of annealing points. + ) + protocol_dict["annealing-npoints"] = ( + 2 # Two annealing points for "system" temperature group. + ) # Linearly change temperature between start and end times. protocol_dict["annealing-time"] = "0 %d" % end_time @@ -609,20 +609,20 @@ def tranform(charge, LJ): "temperature", ]: if name in LambdaValues: - protocol_dict[ - "{:<20}".format("{}-lambdas".format(name)) - ] = " ".join( - list(map("{:.5f}".format, LambdaValues[name].to_list())) + protocol_dict["{:<20}".format("{}-lambdas".format(name))] = ( + " ".join( + list(map("{:.5f}".format, LambdaValues[name].to_list())) + ) ) - protocol_dict[ - "init-lambda-state" - ] = self.protocol.getLambdaIndex() # Current lambda value. - protocol_dict[ - "nstcalcenergy" - ] = self._report_interval # Calculate energies every report_interval steps. - protocol_dict[ - "nstdhdl" - ] = self._report_interval # Write gradients every report_interval steps. + protocol_dict["init-lambda-state"] = ( + self.protocol.getLambdaIndex() + ) # Current lambda value. + protocol_dict["nstcalcenergy"] = ( + self._report_interval + ) # Calculate energies every report_interval steps. + protocol_dict["nstdhdl"] = ( + self._report_interval + ) # Write gradients every report_interval steps. # Handle the combination of multiple distance restraints and perturbation type # of "release_restraint". In this case, the force constant of the "permanent" @@ -829,18 +829,18 @@ def generateSomdConfig( # Free energies. if isinstance(self.protocol, _Protocol._FreeEnergyMixin): if not isinstance(self.protocol, _Protocol.Minimisation): - protocol_dict[ - "constraint" - ] = "hbonds-notperturbed" # Handle hydrogen perturbations. - protocol_dict[ - "energy frequency" - ] = 250 # Write gradients every 250 steps. + protocol_dict["constraint"] = ( + "hbonds-notperturbed" # Handle hydrogen perturbations. + ) + protocol_dict["energy frequency"] = ( + 250 # Write gradients every 250 steps. + ) protocol = [str(x) for x in self.protocol.getLambdaValues()] protocol_dict["lambda array"] = ", ".join(protocol) - protocol_dict[ - "lambda_val" - ] = self.protocol.getLambda() # Current lambda value. + protocol_dict["lambda_val"] = ( + self.protocol.getLambda() + ) # Current lambda value. try: # RBFE res_num = ( @@ -857,9 +857,9 @@ def generateSomdConfig( .value() ) - protocol_dict[ - "perturbed residue number" - ] = res_num # Perturbed residue number. + protocol_dict["perturbed residue number"] = ( + res_num # Perturbed residue number. + ) # Put everything together in a line-by-line format. total_dict = {**protocol_dict, **extra_options} diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py index 6de6095dd..8a381622b 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py +++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_molecule.py @@ -353,10 +353,17 @@ def extract(self, indices, renumber=False, property_map={}): for idx in indices_: selection.select(idx) + # Store the Sire molecule. + sire_mol = self._sire_object + + # Remove the "parameters" property, if it exists. + if sire_mol.hasProperty("parameters"): + sire_mol = ( + sire_mol.edit().removeProperty("parameters").commit().molecule() + ) + partial_mol = ( - _SireMol.PartialMolecule(self._sire_object, selection) - .extract() - .molecule() + _SireMol.PartialMolecule(sire_mol, selection).extract().molecule() ) except Exception as e: msg = "Unable to create partial molecule!" @@ -792,7 +799,11 @@ def makeCompatibleWith( if len(matches) < num_atoms0: # Atom names or order might have changed. Try to match by coordinates. matcher = _SireMol.AtomCoordMatcher() - matches = matcher.match(mol0, mol1) + + try: + matches = matcher.match(mol0, mol1) + except: + matches = [] # We need to rename the atoms. is_renamed = True @@ -1003,7 +1014,11 @@ def makeCompatibleWith( matcher = _SireMol.AtomCoordMatcher() # Get the matches for this molecule and append to the list. - match = matcher.match(mol0, mol) + try: + match = matcher.match(mol0, mol) + except: + match = [] + matches.append(match) num_matches += len(match) diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py index 56bf3aebe..7dc882868 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py +++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_system.py @@ -1888,6 +1888,7 @@ def getRestraintAtoms( string = ( "(not water) and (resname " + ",".join(_prot_res) + + "," + ",".join(_nucl_res) + ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)" ) @@ -1943,6 +1944,7 @@ def getRestraintAtoms( string = ( "(not water) and (resname " + ",".join(_prot_res) + + "," + ",".join(_nucl_res) + ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)" ) diff --git a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_utils.py b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_utils.py index 6d735cc65..9f2b3eac3 100644 --- a/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_utils.py +++ b/python/BioSimSpace/Sandpit/Exscientia/_SireWrappers/_utils.py @@ -22,8 +22,8 @@ Utilities. """ -# A set of protein residues. Taken from MDAnalysis. -_prot_res = { +# A list of protein residues. Taken from MDAnalysis. +_prot_res = [ # CHARMM top_all27_prot_lipid.rtf "ALA", "ARG", @@ -135,10 +135,10 @@ "CMET", "CME", "ASF", -} +] -# A set of nucleic acid residues. Taken from MDAnalysis. -_nucl_res = { +# A list of nucleic acid residues. Taken from MDAnalysis. +_nucl_res = [ "ADE", "URA", "CYT", @@ -173,7 +173,7 @@ "RU3", "RG3", "RC3", -} +] # A list of ion elements. _ions = [ diff --git a/python/BioSimSpace/_Config/_amber.py b/python/BioSimSpace/_Config/_amber.py index 2a93e52a8..861fa5d72 100644 --- a/python/BioSimSpace/_Config/_amber.py +++ b/python/BioSimSpace/_Config/_amber.py @@ -31,7 +31,9 @@ from sire.legacy import Units as _SireUnits +from ..Align._squash import _amber_mask_from_indices, _squashed_atom_mapping from .. import Protocol as _Protocol +from ..Protocol._free_energy_mixin import _FreeEnergyMixin from ..Protocol._position_restraint_mixin import _PositionRestraintMixin from ._config import Config as _Config @@ -63,7 +65,13 @@ def __init__(self, system, protocol, property_map={}): super().__init__(system, protocol, property_map=property_map) def createConfig( - self, version=None, is_pmemd=False, extra_options={}, extra_lines=[] + self, + version=None, + is_pmemd=False, + is_pmemd_cuda=False, + explicit_dummies=False, + extra_options={}, + extra_lines=[], ): """ Create the list of configuration strings. @@ -74,6 +82,12 @@ def createConfig( is_pmemd : bool Whether the configuration is for a simulation using PMEMD. + is_pmemd_cuda : bool + Whether the configuration is for a simulation using PMEMD with CUDA. + + explicit_dummies : bool + Whether to keep the dummy atoms explicit at the endstates or remove them. + extra_options : dict A dictionary containing extra options. Overrides the defaults generated by the protocol. @@ -96,6 +110,12 @@ def createConfig( if not isinstance(is_pmemd, bool): raise TypeError("'is_pmemd' must be of type 'bool'.") + if not isinstance(is_pmemd_cuda, bool): + raise TypeError("'is_pmemd_cuda' must be of type 'bool'.") + + if not isinstance(explicit_dummies, bool): + raise TypeError("'explicit_dummies' must be of type 'bool'.") + if not isinstance(extra_options, dict): raise TypeError("'extra_options' must be of type 'dict'.") else: @@ -109,6 +129,14 @@ def createConfig( if not all(isinstance(line, str) for line in extra_lines): raise TypeError("Lines in 'extra_lines' must be of type 'str'.") + # Vaccum simulation. + if not self.hasBox(self._system, self._property_map) or not self.hasWater( + self._system + ): + is_vacuum = True + else: + is_vacuum = False + # Initialise the protocol lines. protocol_lines = [] @@ -134,6 +162,9 @@ def createConfig( # Only read coordinates from file. protocol_dict["ntx"] = 1 + # Initialise a null timestep. + timestep = None + # Minimisation. if isinstance(self._protocol, _Protocol.Minimisation): # Work out the number of steepest descent cycles. @@ -156,8 +187,15 @@ def createConfig( # Report energies every 100 steps. protocol_dict["ntpr"] = 100 else: - # Define the timestep + # Get the time step. timestep = self._protocol.getTimeStep().picoseconds().value() + # For free-energy calculations, we can only use a 1fs time step in + # vacuum. + if isinstance(self._protocol, _FreeEnergyMixin): + if is_vacuum and not is_pmemd_cuda and timestep > 0.001: + raise ValueError( + "AMBER free-energy calculations in vacuum using pmemd must use a 1fs time step." + ) # Set the integration time step. protocol_dict["dt"] = f"{timestep:.3f}" # Number of integration steps. @@ -171,12 +209,14 @@ def createConfig( protocol_dict["ntf"] = 2 # Periodic boundary conditions. - if not self.hasBox() or not self.hasWater(): + if is_vacuum and not ( + is_pmemd_cuda and isinstance(self._protocol, _FreeEnergyMixin) + ): # No periodic box. protocol_dict["ntb"] = 0 # Non-bonded cut-off. protocol_dict["cut"] = "999." - if is_pmemd: + if is_pmemd_cuda: # Use vacuum generalised Born model. protocol_dict["igb"] = "6" else: @@ -197,6 +237,19 @@ def createConfig( else: atom_idxs = restraint + # Convert to a squashed representation, if needed + if isinstance(self._protocol, _FreeEnergyMixin): + atom_mapping0 = _squashed_atom_mapping( + self.system, is_lambda1=False + ) + atom_mapping1 = _squashed_atom_mapping( + self._system, is_lambda1=True + ) + atom_idxs = sorted( + {atom_mapping0[x] for x in atom_idxs if x in atom_mapping0} + | {atom_mapping1[x] for x in atom_idxs if x in atom_mapping1} + ) + # Don't add restraints if there are no atoms to restrain. if len(atom_idxs) > 0: # Generate the restraint mask based on atom indices. @@ -247,13 +300,15 @@ def createConfig( if not isinstance(self._protocol, _Protocol.Minimisation): if self._protocol.getPressure() is not None: # Don't use barostat for vacuum simulations. - if self.hasBox() and self.hasWater(): + if self.hasBox(self._system, self._property_map) and self.hasWater( + self._system + ): # Isotropic pressure scaling. protocol_dict["ntp"] = 1 # Pressure in bar. - protocol_dict[ - "pres0" - ] = f"{self._protocol.getPressure().bar().value():.5f}" + protocol_dict["pres0"] = ( + f"{self._protocol.getPressure().bar().value():.5f}" + ) if isinstance(self._protocol, _Protocol.Equilibration): # Berendsen barostat. protocol_dict["barostat"] = 1 @@ -303,6 +358,45 @@ def createConfig( # Final temperature. protocol_dict["temp0"] = f"{temp:.2f}" + # Free energies. + if isinstance(self._protocol, _FreeEnergyMixin): + # Free energy mode. + protocol_dict["icfe"] = 1 + # Use softcore potentials. + protocol_dict["ifsc"] = 1 + # Remove SHAKE constraints. + protocol_dict["ntf"] = 1 + + # Get the list of lambda values. + lambda_values = [f"{x:.5f}" for x in self._protocol.getLambdaValues()] + + # Number of states in the MBAR calculation. (Number of lambda values.) + protocol_dict["mbar_states"] = len(lambda_values) + + # Lambda values for the MBAR calculation. + protocol_dict["mbar_lambda"] = ", ".join(lambda_values) + + # Current lambda value. + protocol_dict["clambda"] = "{:.5f}".format(self._protocol.getLambda()) + + if isinstance(self._protocol, _Protocol.Production): + # Calculate MBAR energies. + protocol_dict["ifmbar"] = 1 + # Output dVdl + protocol_dict["logdvdl"] = 1 + + # Atom masks. + protocol_dict = { + **protocol_dict, + **self._generate_amber_fep_masks( + self._system, + is_vacuum, + is_pmemd_cuda, + timestep, + explicit_dummies=explicit_dummies, + ), + } + # Put everything together in a line-by-line format. total_dict = {**protocol_dict, **extra_options} dict_lines = [self._protocol.__class__.__name__, "&cntrl"] @@ -389,3 +483,83 @@ def _create_restraint_mask(self, atom_idxs): restraint_mask += f",{idx+1}" return restraint_mask + + def _generate_amber_fep_masks( + self, system, is_vacuum, is_pmemd_cuda, timestep, explicit_dummies=False + ): + """ + Internal helper function which generates timasks and scmasks based + on the system. + + Parameters + ---------- + + system : :class:`System ` + The molecular system. + + is_vacuum : bool + Whether this is a vacuum simulation. + + is_pmemd_cuda : bool + Whether this is a CUDA simulation. + + timestep : float + The timestep of the simulation in femtoseconds. + + explicit_dummies : bool + Whether to keep the dummy atoms explicit at the endstates or remove them. + + Returns + ------- + + option_dict : dict + A dictionary of AMBER-compatible options. + """ + # Get the merged to squashed atom mapping of the whole system for both endpoints. + kwargs = dict(environment=False, explicit_dummies=explicit_dummies) + mcs_mapping0 = _squashed_atom_mapping( + self._system, is_lambda1=False, common=True, dummies=False, **kwargs + ) + mcs_mapping1 = _squashed_atom_mapping( + self._system, is_lambda1=True, common=True, dummies=False, **kwargs + ) + dummy_mapping0 = _squashed_atom_mapping( + self._system, is_lambda1=False, common=False, dummies=True, **kwargs + ) + dummy_mapping1 = _squashed_atom_mapping( + self._system, is_lambda1=True, common=False, dummies=True, **kwargs + ) + + # Generate the TI and dummy masks. + mcs0_indices, mcs1_indices, dummy0_indices, dummy1_indices = [], [], [], [] + for i in range(self._system.nAtoms()): + if i in dummy_mapping0: + dummy0_indices.append(dummy_mapping0[i]) + if i in dummy_mapping1: + dummy1_indices.append(dummy_mapping1[i]) + if i in mcs_mapping0: + mcs0_indices.append(mcs_mapping0[i]) + if i in mcs_mapping1: + mcs1_indices.append(mcs_mapping1[i]) + ti0_indices = mcs0_indices + dummy0_indices + ti1_indices = mcs1_indices + dummy1_indices + + # SHAKE should be used for timestep >= 2 fs. + if timestep is not None and timestep >= 0.002: + no_shake_mask = "" + else: + no_shake_mask = _amber_mask_from_indices(ti0_indices + ti1_indices) + + # Create an option dict with amber masks generated from the above indices. + option_dict = { + "timask1": f'"{_amber_mask_from_indices(ti0_indices)}"', + "timask2": f'"{_amber_mask_from_indices(ti1_indices)}"', + "scmask1": f'"{_amber_mask_from_indices(dummy0_indices)}"', + "scmask2": f'"{_amber_mask_from_indices(dummy1_indices)}"', + "tishake": 0 if is_pmemd_cuda else 1, + "noshakemask": f'"{no_shake_mask}"', + "gti_add_sc": 1, + "gti_bat_sc": 1, + } + + return option_dict diff --git a/python/BioSimSpace/_Config/_config.py b/python/BioSimSpace/_Config/_config.py index 3aea03484..9005dbb78 100644 --- a/python/BioSimSpace/_Config/_config.py +++ b/python/BioSimSpace/_Config/_config.py @@ -79,22 +79,43 @@ def __init__(self, system, protocol, property_map={}): self._protocol = protocol self._property_map = property_map - def hasBox(self): + @staticmethod + def hasBox(system, property_map={}): """ Whether the system has a box. + Parameters + ---------- + + system : :class:`System ` + The molecular system. + + property_map : dict + A dictionary that maps system "properties" to their user defined + values. This allows the user to refer to properties with their + own naming scheme, e.g. { "charge" : "my-charge" } + Returns ------- has_box : bool Whether the system has a simulation box. """ - space_prop = self._property_map.get("space", "space") - if space_prop in self._system._sire_object.propertyKeys(): + + if not isinstance(system, _System): + raise TypeError( + "'system' must be of type 'BioSimSpace._SireWrappers.System'" + ) + + if not isinstance(property_map, dict): + raise TypeError("'property_map' must be of type 'dict'") + + space_prop = property_map.get("space", "space") + if space_prop in system._sire_object.propertyKeys(): try: # Make sure that we have a periodic box. The system will now have # a default cartesian space. - box = self._system._sire_object.property(space_prop) + box = system._sire_object.property(space_prop) has_box = box.isPeriodic() except: has_box = False @@ -104,17 +125,28 @@ def hasBox(self): return has_box - def hasWater(self): + @staticmethod + def hasWater(system): """ Whether the system is contains water molecules. + Parameters + + system : :class:`System ` + The molecular system. + Returns ------- has_water : bool Whether the system contains water molecules. """ - return self._system.nWaterMolecules() > 0 + if not isinstance(system, _System): + raise TypeError( + "'system' must be of type 'BioSimSpace._SireWrappers.System'" + ) + + return system.nWaterMolecules() > 0 def reportInterval(self): """ diff --git a/python/BioSimSpace/_Config/_gromacs.py b/python/BioSimSpace/_Config/_gromacs.py index 010985613..1355b274c 100644 --- a/python/BioSimSpace/_Config/_gromacs.py +++ b/python/BioSimSpace/_Config/_gromacs.py @@ -145,7 +145,9 @@ def createConfig(self, version=None, extra_options={}, extra_lines=[]): protocol_dict["pbc"] = "xyz" # Use Verlet pair lists. protocol_dict["cutoff-scheme"] = "Verlet" - if self.hasBox() and self.hasWater(): + if self.hasBox(self._system, self._property_map) and self.hasWater( + self._system + ): # Use a grid to search for neighbours. protocol_dict["ns-type"] = "grid" # Rebuild neighbour list every 20 steps. @@ -186,7 +188,9 @@ def createConfig(self, version=None, extra_options={}, extra_lines=[]): if not isinstance(self._protocol, _Protocol.Minimisation): if self._protocol.getPressure() is not None: # Don't use barostat for vacuum simulations. - if self.hasBox() and self.hasWater(): + if self.hasBox(self._system, self._property_map) and self.hasWater( + self._system + ): # Barostat type. if version and version >= 2021: protocol_dict["pcoupl"] = "c-rescale" @@ -195,9 +199,9 @@ def createConfig(self, version=None, extra_options={}, extra_lines=[]): # 1ps time constant for pressure coupling. protocol_dict["tau-p"] = 1 # Pressure in bar. - protocol_dict[ - "ref-p" - ] = f"{self._protocol.getPressure().bar().value():.5f}" + protocol_dict["ref-p"] = ( + f"{self._protocol.getPressure().bar().value():.5f}" + ) # Compressibility of water. protocol_dict["compressibility"] = "4.5e-5" else: diff --git a/python/BioSimSpace/_Config/_somd.py b/python/BioSimSpace/_Config/_somd.py index 12ce38b7d..a5ba74106 100644 --- a/python/BioSimSpace/_Config/_somd.py +++ b/python/BioSimSpace/_Config/_somd.py @@ -173,10 +173,12 @@ def createConfig(self, extra_options={}, extra_lines=[]): pass # Periodic boundary conditions. - if self.hasWater(): + if self.hasWater(self._system): # Solvated box. protocol_dict["reaction field dielectric"] = "78.3" - if not self.hasBox() or not self.hasWater(): + if not self.hasBox(self._system, self._property_map) or not self.hasWater( + self._system + ): # No periodic box. protocol_dict["cutoff type"] = "cutoffnonperiodic" else: @@ -199,7 +201,9 @@ def createConfig(self, extra_options={}, extra_lines=[]): if not isinstance(self._protocol, _Protocol.Minimisation): if self._protocol.getPressure() is not None: # Don't use barostat for vacuum simulations. - if self.hasBox() and self.hasWater(): + if self.hasBox(self._system, self._property_map) and self.hasWater( + self._system + ): # Enable barostat. protocol_dict["barostat"] = True pressure = self._protocol.getPressure().atm().value() diff --git a/python/BioSimSpace/_SireWrappers/_molecule.py b/python/BioSimSpace/_SireWrappers/_molecule.py index 089c88146..6645c54ce 100644 --- a/python/BioSimSpace/_SireWrappers/_molecule.py +++ b/python/BioSimSpace/_SireWrappers/_molecule.py @@ -353,10 +353,17 @@ def extract(self, indices, renumber=False, property_map={}): for idx in indices_: selection.select(idx) + # Store the Sire molecule. + sire_mol = self._sire_object + + # Remove the "parameters" property, if it exists. + if sire_mol.hasProperty("parameters"): + sire_mol = ( + sire_mol.edit().removeProperty("parameters").commit().molecule() + ) + partial_mol = ( - _SireMol.PartialMolecule(self._sire_object, selection) - .extract() - .molecule() + _SireMol.PartialMolecule(sire_mol, selection).extract().molecule() ) except Exception as e: msg = "Unable to create partial molecule!" @@ -748,7 +755,11 @@ def makeCompatibleWith( if len(matches) < num_atoms0: # Atom names or order might have changed. Try to match by coordinates. matcher = _SireMol.AtomCoordMatcher() - matches = matcher.match(mol0, mol1) + + try: + matches = matcher.match(mol0, mol1) + except: + matches = [] # We need to rename the atoms. is_renamed = True @@ -959,7 +970,11 @@ def makeCompatibleWith( matcher = _SireMol.AtomCoordMatcher() # Get the matches for this molecule and append to the list. - match = matcher.match(mol0, mol) + try: + match = matcher.match(mol0, mol) + except: + match = [] + matches.append(match) num_matches += len(match) @@ -1577,7 +1592,11 @@ def _fixCharge(self, property_map={}): self._sire_object = edit_mol.commit() def _toRegularMolecule( - self, property_map={}, is_lambda1=False, convert_amber_dummies=False + self, + property_map={}, + is_lambda1=False, + convert_amber_dummies=False, + generate_intrascale=False, ): """ Internal function to convert a merged molecule to a regular molecule. @@ -1599,6 +1618,9 @@ def _toRegularMolecule( non-FEP simulations. This will replace the "du" ambertype and "Xx" element with the properties from the other end state. + generate_intrascale : bool + Whether to regenerate the intrascale matrix. + Returns ------- @@ -1612,6 +1634,9 @@ def _toRegularMolecule( if not isinstance(convert_amber_dummies, bool): raise TypeError("'convert_amber_dummies' must be of type 'bool'") + if not isinstance(generate_intrascale, bool): + raise TypeError("'generate_intrascale' must be of type 'bool'") + if is_lambda1: lam = "1" else: @@ -1694,6 +1719,17 @@ def _toRegularMolecule( mol = mol.removeProperty("element0").molecule() mol = mol.removeProperty("element1").molecule() + if generate_intrascale: + # First we regenerate the connectivity based on the bonds. + conn = _SireMol.Connectivity(mol.info()).edit() + for bond in mol.property("bond").potentials(): + conn.connect(bond.atom0(), bond.atom1()) + mol.setProperty("connectivity", conn.commit()) + + # Now we have the correct connectivity, we can regenerate the exclusions. + gro_sys = _SireIO.GroTop(_System(mol)._sire_object).toSystem() + mol.setProperty("intrascale", gro_sys[0].property("intrascale")) + # Return the updated molecule. return Molecule(mol.commit()) diff --git a/python/BioSimSpace/_SireWrappers/_system.py b/python/BioSimSpace/_SireWrappers/_system.py index 380a3b736..2d458890b 100644 --- a/python/BioSimSpace/_SireWrappers/_system.py +++ b/python/BioSimSpace/_SireWrappers/_system.py @@ -1809,6 +1809,7 @@ def getRestraintAtoms( string = ( "(not water) and (resname " + ",".join(_prot_res) + + "," + ",".join(_nucl_res) + ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)" ) @@ -1864,6 +1865,7 @@ def getRestraintAtoms( string = ( "(not water) and (resname " + ",".join(_prot_res) + + "," + ",".join(_nucl_res) + ") and (atomname N,CA,C,O,P,/C5'/,/C3'/,/O3'/,/O5'/)" ) diff --git a/python/BioSimSpace/_SireWrappers/_utils.py b/python/BioSimSpace/_SireWrappers/_utils.py index 6d735cc65..9f2b3eac3 100644 --- a/python/BioSimSpace/_SireWrappers/_utils.py +++ b/python/BioSimSpace/_SireWrappers/_utils.py @@ -22,8 +22,8 @@ Utilities. """ -# A set of protein residues. Taken from MDAnalysis. -_prot_res = { +# A list of protein residues. Taken from MDAnalysis. +_prot_res = [ # CHARMM top_all27_prot_lipid.rtf "ALA", "ARG", @@ -135,10 +135,10 @@ "CMET", "CME", "ASF", -} +] -# A set of nucleic acid residues. Taken from MDAnalysis. -_nucl_res = { +# A list of nucleic acid residues. Taken from MDAnalysis. +_nucl_res = [ "ADE", "URA", "CYT", @@ -173,7 +173,7 @@ "RU3", "RG3", "RC3", -} +] # A list of ion elements. _ions = [ diff --git a/recipes/biosimspace/template.yaml b/recipes/biosimspace/template.yaml index 4e3a7edeb..fd9f0a4c4 100644 --- a/recipes/biosimspace/template.yaml +++ b/recipes/biosimspace/template.yaml @@ -27,7 +27,7 @@ test: - SIRE_SILENT_PHONEHOME requires: - pytest <8 - - black 23 # [linux and x86_64 and py==312] + - black 24 # [linux and x86_64 and py==312] - pytest-black # [linux and x86_64 and py==312] - ambertools # [linux and x86_64] - gromacs # [linux and x86_64] diff --git a/tests/Align/test_squash.py b/tests/Align/test_squash.py new file mode 100644 index 000000000..ac829a2fc --- /dev/null +++ b/tests/Align/test_squash.py @@ -0,0 +1,204 @@ +import os +import numpy as np +import pickle +import pytest + +import sire + +from sire.maths import Vector + +import BioSimSpace as BSS + +# Make sure AMBER is installed. +if BSS._amber_home is not None: + exe = "%s/bin/sander" % BSS._amber_home + if os.path.isfile(exe): + has_amber = True + else: + has_amber = False +else: + has_amber = False + + +@pytest.fixture(scope="session") +def perturbed_system(): + # N_atoms are: 12, 15, 18, 21, 24, 27 and 30. + mol_smiles = [ + "c1ccccc1", + "c1ccccc1C", + "c1ccccc1CC", + "c1ccccc1CCC", + "c1ccccc1CCCC", + "c1ccccc1CCCCC", + "c1ccccc1CCCCCC", + ] + mols = [BSS.Parameters.gaff(smi).getMolecule() for smi in mol_smiles] + pert_mols = [ + mols[0], + BSS.Align.merge(mols[1], mols[2]), + mols[3], + mols[4], + BSS.Align.merge(mols[5], mols[6]), + ] + system = BSS._SireWrappers.System(pert_mols) + return system + + +@pytest.fixture(scope="session") +def dual_topology_system(): + mol_smiles = ["c1ccccc1", "c1ccccc1C"] + mols = [BSS.Parameters.gaff(smi).getMolecule() for smi in mol_smiles] + pertmol = BSS.Align.merge(mols[0], mols[1], mapping={0: 0}) + c = pertmol._sire_object.cursor() + # Translate all atoms so that we have different coordinates between both endstates + for atom in c.atoms(): + atom["coordinates1"] = atom["coordinates0"] + Vector(1, 1, 1) + pertmol = BSS._SireWrappers.Molecule(c.commit()) + system = pertmol.toSystem() + return system + + +@pytest.fixture +def perturbed_tripeptide(): + return pickle.load(open(f"tests/input/merged_tripeptide.pickle", "rb")) + + +@pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.") +@pytest.mark.parametrize( + "explicit,expected_n_atoms", + [ + (False, [12, 21, 24, 15, 18, 27, 30]), + (True, [12, 21, 24, 18, 18, 30, 30]), + ], +) +def test_squash(perturbed_system, explicit, expected_n_atoms): + squashed_system, mapping = BSS.Align._squash._squash( + perturbed_system, explicit_dummies=explicit + ) + assert len(squashed_system) == 7 + n_atoms = [mol.nAtoms() for mol in squashed_system] + assert squashed_system[-2].getResidues()[0].name() == "LIG" + assert squashed_system[-1].getResidues()[0].name() == "LIG" + # First we must have the unperturbed molecules, and then the perturbed ones. + assert n_atoms == expected_n_atoms + python_mapping = {k.value(): v.value() for k, v in mapping.items()} + assert python_mapping == {0: 0, 2: 1, 3: 2} + + +@pytest.mark.parametrize("explicit", [False, True]) +def test_squash_multires(perturbed_tripeptide, explicit): + squashed_system, mapping = BSS.Align._squash._squash( + perturbed_tripeptide, explicit_dummies=explicit + ) + assert len(squashed_system) == 1 + assert len(squashed_system[0].getResidues()) == 4 + + +@pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.") +@pytest.mark.parametrize("is_lambda1", [False, True]) +def test_squashed_molecule_mapping(perturbed_system, is_lambda1): + res = BSS.Align._squash._squashed_molecule_mapping( + perturbed_system, is_lambda1=is_lambda1 + ) + if not is_lambda1: + expected = {0: 0, 2: 1, 3: 2, 1: 3, 4: 5} + else: + expected = {0: 0, 2: 1, 3: 2, 1: 4, 4: 6} + assert res == expected + + +@pytest.mark.parametrize("is_lambda1", [False, True]) +def test_squashed_atom_mapping_implicit(perturbed_tripeptide, is_lambda1): + res = BSS.Align._squash._squashed_atom_mapping( + perturbed_tripeptide, is_lambda1=is_lambda1, explicit_dummies=False + ) + if not is_lambda1: + merged_indices = list(range(16)) + list(range(16, 30)) + list(range(43, 51)) + squashed_indices = list(range(16)) + list(range(16, 30)) + list(range(30, 38)) + else: + merged_indices = ( + list(range(16)) + + list(range(16, 21)) + + list(range(23, 26)) + + list(range(30, 43)) + + list(range(43, 51)) + ) + squashed_indices = list(range(16)) + list(range(38, 59)) + list(range(30, 38)) + expected = dict(zip(merged_indices, squashed_indices)) + assert res == expected + + +@pytest.mark.parametrize("is_lambda1", [False, True]) +def test_squashed_atom_mapping_explicit(perturbed_tripeptide, is_lambda1): + res = BSS.Align._squash._squashed_atom_mapping( + perturbed_tripeptide, is_lambda1=is_lambda1, explicit_dummies=True + ) + merged_indices = list(range(51)) + if not is_lambda1: + squashed_indices = list(range(16)) + list(range(16, 43)) + list(range(43, 51)) + else: + squashed_indices = list(range(16)) + list(range(51, 78)) + list(range(43, 51)) + expected = dict(zip(merged_indices, squashed_indices)) + assert res == expected + + +@pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.") +@pytest.mark.parametrize("explicit", [False, True]) +def test_unsquash(dual_topology_system, explicit): + squashed_system, mapping = BSS.Align._squash._squash( + dual_topology_system, explicit_dummies=explicit + ) + new_perturbed_system = BSS.Align._squash._unsquash( + dual_topology_system, squashed_system, mapping, explicit_dummies=explicit + ) + assert [ + mol0.nAtoms() == mol1.nAtoms() + for mol0, mol1 in zip(dual_topology_system, new_perturbed_system) + ] + assert [ + mol0.isPerturbable() == mol1.isPerturbable() + for mol0, mol1 in zip(dual_topology_system, new_perturbed_system) + ] + if explicit: + # Check that we have loaded the correct coordinates + coords0_before = sire.io.get_coords_array( + dual_topology_system[0]._sire_object, map={"coordinates": "coordinates0"} + ) + coords1_before = sire.io.get_coords_array( + dual_topology_system[0]._sire_object, map={"coordinates": "coordinates1"} + ) + coords0_after = sire.io.get_coords_array( + new_perturbed_system[0]._sire_object, map={"coordinates": "coordinates0"} + ) + coords1_after = sire.io.get_coords_array( + new_perturbed_system[0]._sire_object, map={"coordinates": "coordinates1"} + ) + + # The coordinates at the first endstate should be completely preserved + # Because in this case they are either common core, or separate dummies at lambda = 0 + assert np.allclose(coords0_before, coords0_after) + + # The coordinates at the first endstate should be partially preserved + # The common core must have the same coordinates as lambda = 0 + # Here this is just a single atom in the beginning + # The extra atoms which are dummies at lambda = 0 have separate coordinates here + assert np.allclose(coords0_before[:1, :], coords1_after[:1, :]) + assert np.allclose(coords1_before[1:, :], coords1_after[1:, :]) + + +@pytest.mark.parametrize("explicit", [False, True]) +def test_unsquash_multires(perturbed_tripeptide, explicit): + squashed_system, mapping = BSS.Align._squash._squash( + perturbed_tripeptide, explicit_dummies=explicit + ) + new_perturbed_system = BSS.Align._squash._unsquash( + perturbed_tripeptide, squashed_system, mapping, explicit_dummies=explicit + ) + assert [ + mol0.nAtoms() == mol1.nAtoms() + for mol0, mol1 in zip(perturbed_tripeptide, new_perturbed_system) + ] + assert [ + mol0.isPerturbable() == mol1.isPerturbable() + for mol0, mol1 in zip(perturbed_tripeptide, new_perturbed_system) + ] diff --git a/tests/FreeEnergy/test_relative.py b/tests/FreeEnergy/test_relative.py index f93f49e61..6d01fe81f 100644 --- a/tests/FreeEnergy/test_relative.py +++ b/tests/FreeEnergy/test_relative.py @@ -54,8 +54,9 @@ def expected_results(): """A dictionary of expected FEP results.""" return { - "somd": {"mbar": -6.3519, "ti": -6.3209}, + "amber": {"mbar": -12.5939, "ti": -13.6850}, "gromacs": {"mbar": -6.0238, "ti": -8.4158}, + "somd": {"mbar": -6.3519, "ti": -6.3209}, } @@ -73,7 +74,7 @@ def test_setup_gromacs(perturbable_system): @pytest.mark.skipif( has_alchemlyb is False, reason="Requires alchemlyb to be installed." ) -@pytest.mark.parametrize("engine", ["somd", "gromacs"]) +@pytest.mark.parametrize("engine", ["amber", "gromacs", "somd"]) @pytest.mark.parametrize("estimator", ["mbar", "ti"]) def test_analysis(fep_output, engine, estimator, expected_results): """Test that the free energy analysis works as expected.""" diff --git a/tests/Process/test_amber.py b/tests/Process/test_amber.py index 89355c80b..a6626047e 100644 --- a/tests/Process/test_amber.py +++ b/tests/Process/test_amber.py @@ -1,5 +1,9 @@ from collections import OrderedDict + +import math import pytest +import shutil +import socket import BioSimSpace as BSS @@ -31,6 +35,28 @@ def large_protein_system(): ) +@pytest.fixture(scope="module") +def perturbable_system(): + """Re-use the same perturbable system for each test.""" + return BSS.IO.readPerturbableSystem( + f"{url}/perturbable_system0.prm7", + f"{url}/perturbable_system0.rst7", + f"{url}/perturbable_system1.prm7", + f"{url}/perturbable_system1.rst7", + ) + + +@pytest.fixture(scope="module") +def solvated_perturbable_system(): + """Re-use the same solvated perturbable system for each test.""" + return BSS.IO.readPerturbableSystem( + f"{url}/solvated_perturbable_system0.prm7", + f"{url}/solvated_perturbable_system0.rst7", + f"{url}/solvated_perturbable_system1.prm7", + f"{url}/solvated_perturbable_system1.rst7", + ) + + @pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.") @pytest.mark.parametrize("restraint", restraints) def test_minimise(system, restraint): @@ -286,3 +312,203 @@ def run_process(system, protocol, check_data=False): for k, v in data.items(): assert len(v) == nrec + + +@pytest.mark.skipif( + has_amber is False, reason="Requires AMBER and pyarrow to be installed." +) +@pytest.mark.parametrize( + "protocol", + [ + BSS.Protocol.FreeEnergy(temperature=298 * BSS.Units.Temperature.kelvin), + BSS.Protocol.FreeEnergyMinimisation(), + ], +) +def test_parse_fep_output(perturbable_system, protocol): + """Make sure that we can correctly parse AMBER FEP output.""" + + from sire.legacy.Base import findExe + + # Copy the system. + system_copy = perturbable_system.copy() + + # Use the first instance of sander in the path so that we can + # test without pmemd. + exe = findExe("sander").absoluteFilePath() + process = BSS.Process.Amber(system_copy, protocol, exe=exe) + + # Assign the path to the output file. + if isinstance(protocol, BSS.Protocol.FreeEnergy): + out_file = "tests/output/amber_fep.out" + else: + out_file = "tests/output/amber_fep_min.out" + + # Copy the existing output file into the working directory. + shutil.copyfile(out_file, process.workDir() + "/amber.out") + + # Update the stdout record dictionaries. + process.stdout(0) + + # Get back the records for each region and soft-core part. + records_ti0 = process.getRecords(region=0) + records_sc0 = process.getRecords(region=0, soft_core=True) + records_ti1 = process.getRecords(region=1) + records_sc1 = process.getRecords(region=1, soft_core=True) + + # Make sure NSTEP is present. + assert "NSTEP" in records_ti0 + + # Get the number of records. + num_records = len(records_ti0["NSTEP"]) + + # Now make sure that the records for the two TI regions contain the + # same number of values. + for v0, v1 in zip(records_ti0.values(), records_ti1.values()): + assert len(v0) == len(v1) == num_records + + # Now check that are records for the soft-core parts contain the correct + # number of values. + for v in records_sc0.values(): + assert len(v) == num_records + for k, v in records_sc1.items(): + assert len(v) == num_records + if isinstance(protocol, BSS.Protocol.FreeEnergy): + assert len(records_sc0) == len(records_sc1) + else: + assert len(records_sc0) == 0 + assert len(records_sc1) != 0 + + +@pytest.mark.skipif( + socket.gethostname() != "porridge", + reason="Local test requiring pmemd installation.", +) +def test_pmemd(system): + """Single-point energy tests for pmemd.""" + + # Path to the pmemd conda environment bin directory. + bin_dir = "/home/lester/.conda/envs/pmemd/bin" + + # Single-point minimisation protocol. + protocol = BSS.Protocol.Minimisation(steps=1) + + # First perform single-point comparisons in solvent. + + # Compute the single-point energy using sander. + process = BSS.Process.Amber(system, protocol) + process.start() + process.wait() + assert not process.isError() + nrg_sander = process.getTotalEnergy().value() + + # Compute the single-point energy using pmemd. + process = BSS.Process.Amber(system, protocol, exe=f"{bin_dir}/pmemd") + process.start() + process.wait() + assert not process.isError() + nrg_pmemd = process.getTotalEnergy().value() + + # Compute the single-point energy using pmemd.cuda. + process = BSS.Process.Amber(system, protocol, exe=f"{bin_dir}/pmemd.cuda") + process.start() + process.wait() + assert not process.isError() + nrg_pmemd_cuda = process.getTotalEnergy().value() + + # Check that the energies are the same. + assert math.isclose(nrg_sander, nrg_pmemd, rel_tol=1e-4) + assert math.isclose(nrg_sander, nrg_pmemd_cuda, rel_tol=1e-4) + + # Now perform single-point comparisons in vacuum. + + vac_system = system[0].toSystem() + + # Compute the single-point energy using sander. + process = BSS.Process.Amber(vac_system, protocol) + process.start() + process.wait() + assert not process.isError() + nrg_sander = process.getTotalEnergy().value() + + # Compute the single-point energy using pmemd. + process = BSS.Process.Amber(vac_system, protocol, exe=f"{bin_dir}/pmemd") + process.start() + process.wait() + assert not process.isError() + nrg_pmemd = process.getTotalEnergy().value() + + # Compute the single-point energy using pmemd.cuda. + process = BSS.Process.Amber(vac_system, protocol, exe=f"{bin_dir}/pmemd.cuda") + process.start() + process.wait() + assert not process.isError() + nrg_pmemd_cuda = process.getTotalEnergy().value() + + # Check that the energies are the same. + assert math.isclose(nrg_sander, nrg_pmemd, rel_tol=1e-4) + assert math.isclose(nrg_sander, nrg_pmemd_cuda, rel_tol=1e-4) + + +@pytest.mark.skipif( + socket.gethostname() != "porridge", + reason="Local test requiring pmemd installation.", +) +def test_pmemd_fep(solvated_perturbable_system): + """Single-point FEP energy tests for pmemd.""" + + # Path to the pmemd conda environment bin directory. + bin_dir = "/home/lester/.conda/envs/pmemd/bin" + + # Single-point minimisation protocol. + protocol = BSS.Protocol.FreeEnergyMinimisation(steps=1) + + # First perform single-point comparisons in solvent. + + # Compute the single-point energy using pmemd. + process = BSS.Process.Amber( + solvated_perturbable_system, protocol, exe=f"{bin_dir}/pmemd" + ) + process.start() + process.wait() + assert not process.isError() + nrg_pmemd = process.getTotalEnergy().value() + + # Compute the single-point energy using pmemd.cuda. + process = BSS.Process.Amber( + solvated_perturbable_system, protocol, exe=f"{bin_dir}/pmemd.cuda" + ) + process.start() + process.wait() + assert not process.isError() + nrg_pmemd_cuda = process.getTotalEnergy().value() + + # Check that the energies are the same. + assert math.isclose(nrg_pmemd, nrg_pmemd_cuda, rel_tol=1e-4) + + # Now perform single-point comparisons in vacuum. + + vac_system = solvated_perturbable_system[0].toSystem() + + # Compute the single-point energy using pmemd. + process = BSS.Process.Amber( + vac_system, protocol, exe=f"{bin_dir}/pmemd", extra_options={"gti_bat_sc": 2} + ) + process.start() + process.wait() + assert not process.isError() + nrg_pmemd = process.getTotalEnergy().value() + + # Compute the single-point energy using pmemd.cuda. + process = BSS.Process.Amber( + vac_system, + protocol, + exe=f"{bin_dir}/pmemd.cuda", + extra_options={"gti_bat_sc": 2}, + ) + process.start() + process.wait() + assert not process.isError() + nrg_pmemd_cuda = process.getTotalEnergy().value() + + # Check that the energies are the same. + assert math.isclose(nrg_pmemd, nrg_pmemd_cuda, rel_tol=1e-3) diff --git a/tests/input/merged_tripeptide.pickle b/tests/input/merged_tripeptide.pickle new file mode 100644 index 000000000..20abb1d64 Binary files /dev/null and b/tests/input/merged_tripeptide.pickle differ diff --git a/tests/output/amber_fep.out b/tests/output/amber_fep.out new file mode 100644 index 000000000..a17a4b91a --- /dev/null +++ b/tests/output/amber_fep.out @@ -0,0 +1,6720 @@ + + ------------------------------------------------------- + Amber 22 PMEMD 2022 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 22 + +| Executable base on git commit: 5582ead046263fa35196b75ad7a34d5162126b1e +| Compiled date/time: Wed May 17 14:14:31 2023 +| Compiled on: rioja-rutgers-edu +| Compiled by: taisung + +| Run on 05/22/2023 at 11:35:03 + +| Executable path: /usr/bin/pmemd.cuda.MPI +| Working directory: /scratch/protein_lig_30~lig_30a__Split1/free/Production +| Hostname: ip-10-70-134-167.ec2.internal + +| WARNING: Stack usage limited by a hard resource limit of 10485760 bytes! +| If segment violations occur, get your sysadmin to increase the limit. + [-O]verwriting output + +File Assignments: +| MDIN: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +| MDOUT: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +| INPCRD: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +| PARM: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +| RESTRT: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +| REFC: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +| MDVEL: mdvel.000 +| MDEN: mden.000 +| MDCRD: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +| MDINFO: /scratch/protein_lig_30~lig_30a__Split1/free/Production/lambda_0.0000/ +|LOGFILE: logfile.000 +| MDFRC: mdfrc.000 + + + Here is the input file: + +FreeEnergy +&cntrl + ntpr=200, + ntwr=10000, + ntwx=10000, + ntxo=2, + irest=1, + ntx=5, + dt=0.002, + nstlim=1000, + ntc=2, + ntf=1, + cut=8.0, + iwrap=1, + ntr=1, + restraint_wt=10.0, + restraintmask="@6433,6470,6489-6490", + ntp=1, + pres0=1.01325, + barostat=2, + ntt=3, + gamma_ln=1.00000, + temp0=298.00, + icfe=1, + ifsc=1, + mbar_states=16, + mbar_lambda=0.00000, 0.06667, 0.13333, 0.20000, 0.26667, 0.33333, 0.40000, 0 + clambda=0.00000, + ifmbar=1, + logdvdl=1, + timask1="@6412-6455,6500", + timask2="@6456-6499,6501", + scmask1="@6453-6455", + scmask2="@6497-6499", + ig=-1, + numexchg=10, + gremd_acyc=1, + scalpha=0.5, + scbeta=1.0, + tishake=2, + gti_cut=1, + gti_output=1, + gti_add_sc=25, + gti_scale_beta=1, + gti_cut_sc_on=6, + gti_cut_sc_off=8, + gti_lam_sch=1, + gti_ele_sc=1, + gti_vdw_sc=1, + gti_cut_sc=2, + gti_ele_exp=2, + gti_vdw_exp=2, + gti_explicit_du=1, + gti_syn_mass=1, +/ + + +Note: ig = -1. Setting random seed to 958728 based on wallclock time in + microseconds and disabling the synchronization of random numbers + between tasks to improve performance. +| irandom = 1, using AMBER's internal random number generator (default). + +|--------------------- INFORMATION ---------------------- +| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. +| Version 18.0.0 +| +| 03/25/2018 +| +| Implementation by: +| Ross C. Walker (SDSC) +| Scott Le Grand (nVIDIA) +| +| Version 18 performance extensions by: +| David Cerutti (Rutgers) +| +| Precision model in use: +| [SPFP] - Single Precision Forces, 64-bit Fixed Point +| Accumulation. (Default) +| +|-------------------------------------------------------- + +|----------------- CITATION INFORMATION ----------------- +| +| When publishing work that utilized the CUDA version +| of AMBER, please cite the following in addition to +| the regular AMBER citations: +| +| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan +| Poole; Scott Le Grand; Ross C. Walker "Routine +| microsecond molecular dynamics simulations with +| AMBER - Part II: Particle Mesh Ewald", J. Chem. +| Theory Comput., 2013, 9 (9), pp3878-3888, +| DOI: 10.1021/ct400314y. +| +| - Andreas W. Goetz; Mark J. Williamson; Dong Xu; +| Duncan Poole; Scott Le Grand; Ross C. Walker +| "Routine microsecond molecular dynamics simulations +| with AMBER - Part I: Generalized Born", J. Chem. +| Theory Comput., 2012, 8 (5), pp1542-1555. +| +| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker +| "SPFP: Speed without compromise - a mixed precision +| model for GPU accelerated molecular dynamics +| simulations.", Comp. Phys. Comm., 2013, 184 +| pp374-380, DOI: 10.1016/j.cpc.2012.09.022 +| +| When publishing work that utilized the CUDA version +| of TI, BAR, MBAR or FEP please cite the following +| publications in addition to the regular AMBER +| GPU citations: +| +| - Daniel J. Mermelstein; Charles Lin; Gard Nelson; +| Rachael Kretsch; J. Andrew McCammon; Ross C. Walker +| "Fast and Flexible GPU Accelerated Binding +| Free Energy Calculations within the AMBER Molecular +| Dynamics Package" J. Comp. Chem., 2018, +| DOI: 10.1002/jcc.25187 +| +| - Tai-Sung Lee; Yuan Hu; Brad Sherborne; Zhuyan Guo; +| Darrin M. York +| "Toward Fast and Accurate Binding Affinity Prediction with +| pmemdGTI: An Efficient Implementation of GPU-Accelerated +| Thermodynamic Integration" +| J. Chem. Theory Comput., 2017, 13 (7), 3077 +| +| +|-------------------------------------------------------- + +|------------------- GPU DEVICE INFO -------------------- +| +| Task ID: 0 +| CUDA_VISIBLE_DEVICES: not set +| CUDA Capable Devices Detected: 2 +| CUDA Device ID in use: 0 +| CUDA Device Name: Tesla M60 +| CUDA Device Global Mem Size: 7612 MB +| CUDA Device Num Multiprocessors: 16 +| CUDA Device Core Freq: 1.18 GHz +| +|-------------------------------------------------------- + +|---------------- GPU PEER TO PEER INFO ----------------- +| +| Peer to Peer support: ENABLED +| +| NCCL support: DISABLED +| +|-------------------------------------------------------- + + +| Conditional Compilation Defines Used: +| MPI +| PUBFFT +| BINTRAJ +| CUDA +| EMIL + +| Largest sphere to fit in unit cell has radius = 20.145 + +| New format PARM file being parsed. +| Version = 1.000 Date = 05/22/23 Time = 11:34:48 + +| Note: 1-4 EEL scale factors are being read from the topology file. + +| Note: 1-4 VDW scale factors are being read from the topology file. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 6501 NTYPES = 13 NBONH = 6441 MBONA = 51 + NTHETH = 89 MTHETA = 70 NPHIH = 201 MPHIA = 143 + NHPARM = 0 NPARM = 0 NNB = 9019 NRES = 2149 + NBONA = 51 NTHETA = 70 NPHIA = 143 NUMBND = 17 + NUMANG = 13 NPTRA = 29 NATYP = 14 NPHB = 0 + IFBOX = 1 NMXRS = 44 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 8 8 8 +| Direct force subcell size = 5.0364 5.0364 5.0364 + + BOX TYPE: RECTILINEAR + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + + + +General flags: + imin = 0, nmropt = 0 + +Replica exchange + numexchg= 10, rem= 3 + +Nature and format of input: + ntx = 5, irest = 1, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 200, ntrx = 1, ntwr = 10000 + iwrap = 1, ntwx = 10000, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 1, ntb = 2, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 1 + restraint_wt = 10.00000 + +Molecular dynamics: + nstlim = 1000, nscm = 0, nrespa = 1 + t = 0.00000, dt = 0.00200, vlimit = -1.00000 + +Langevin dynamics temperature regulation: + ig = 958728 + temp0 = 298.00000, tempi = 0.00000, gamma_ln= 1.00000 + +Pressure regulation: + ntp = 1 + pres0 = 1.01325, comp = 44.60000, taup = 1.00000 + Monte-Carlo Barostat: + mcbarint = 100 + +SHAKE: + ntc = 2, jfastw = 0 + tol = 0.00001 + +Free energy options: + icfe = 1, ifsc = 1, klambda = 1 + clambda = 0.0000, scalpha = 0.5000, scbeta = 1.0000 + sceeorder = 2 + dynlmb = 0.0000 logdvdl = 1 + +FEP MBAR options: + ifmbar = 1, bar_intervall = 100 + mbar_states = 16 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 200 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 1 + Box X = 40.291 Box Y = 40.291 Box Z = 40.291 + Alpha = 90.000 Beta = 90.000 Gamma = 90.000 + NFFT1 = 48 NFFT2 = 48 NFFT3 = 48 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + +| PMEMD ewald parallel performance parameters: +| block_fft = 0 +| fft_blk_y_divisor = 2 +| excl_recip = 0 +| excl_master = 0 +| atm_redist_freq = 320 + + LOADING THE CONSTRAINED ATOMS AS GROUPS + + + 5. REFERENCE ATOM COORDINATES + + + Mask @6433,6470,6489-6490; matches 4 atoms + TI Mask 1 @6412-6455,6500; matches 45 atoms + TI Mask 2 @6456-6499,6501; matches 45 atoms + TI region 1: 6456 atoms + TI region 2: 6456 atoms + SC Mask 1 @6453-6455; matches 3 atoms + SC Mask 2 @6497-6499; matches 3 atoms + + MBAR - lambda values considered: + 16 total: 0.0000 0.0667 0.1333 0.2000 0.2667 0.3333 0.4000 0.4667 0.5333 0.6000 0.6667 0.7333 0.8000 0.8667 0.9333 1.0000 + Extra energies will be computed 10 times. + +|-------------------------------------------------------------------------------------------- +| Extra TI control variables +| gti_add_sc = 25, gti_ele_gauss = 0, gti_auto_alpha = 0, gti_scale_beta = 1 +| gti_ele_exp = 2, gti_vdw_exp = 2, gti_ele_sc = 1, gti_vdw_sc = 1 +| gti_cut = 1, gti_cut_sc = 2 +, gti_explicit_du = 1 +| gti_cut_sc_on = 6.0000, gti_cut_sc_off = 8.0000 +|-------------------------------------------------------------------------------------------- + +| MONTE CARLO BAROSTAT IMPORTANT NOTE: +| The Monte-Carlo barostat does not require the virial to adjust the system volume. +| Since it is an expensive calculation, it is skipped for efficiency. A side-effect +| is that the reported pressure is always 0 because it is not calculated. + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + + + begin time read from input coords = 0.000 ps + + +| REMD: Pressure/volume correction to exchange calc active for TREMD/HREMD. + Molecule 2146 is partially softcore + Molecule 2147 is partially softcore + Molecule 2148 is partially softcore + Molecule 2149 is partially softcore + Number of triangulated 3-point waters found: 2133 + WARNING: SHAKEn bond for atoms 6413 6453 is partially softcore. + WARNING: SHAKEn bond for atoms 6413 6454 is partially softcore. + WARNING: SHAKEn bond for atoms 6413 6455 is partially softcore. + WARNING: SHAKEn bond for atoms 6457 6497 is partially softcore. + WARNING: SHAKEn bond for atoms 6457 6498 is partially softcore. + WARNING: SHAKEn bond for atoms 6457 6499 is partially softcore. + Coordinates for common atoms will be synchronized from V0. + Consider using noshake mask or disabling SHAKE. + + Number of shake restraints removed in TI region 1 : 0 + Number of shake restraints removed in TI region 2 : 0 + + Sum of charges for TI region 1 = 0.61820003 + Skip neutralizing charges... + + + Sum of charges for TI region 2 = 0.00000000 + Skip neutralizing charges... + +| Dynamic Memory, Types Used: +| Reals 599438 +| Integers 475900 + +| Nonbonded Pairs Initial Allocation: 1482228 + +| GPU memory information (estimate): +| KB of GPU memory in use: 49385 +| KB of CPU memory in use: 19049 + +| Running AMBER/MPI version on 1 MPI task + + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + DOF for the SC part 1 of the system: 6 + SHAKE constraints in the SC region: 3 + DOF for the SC part 2 of the system: 6 + SHAKE constraints in the SC region: 3 + +MBAR Energy analysis: +Energy at 0.0000 = -21577.662473 +Energy at 0.0667 = -21575.016620 +Energy at 0.1333 = -21558.650663 +Energy at 0.2000 = -21520.306786 +Energy at 0.2667 = -21456.804779 +Energy at 0.3333 = -21369.086296 +Energy at 0.4000 = -21261.221098 +Energy at 0.4667 = -21139.573946 +Energy at 0.5333 = -21011.890002 +Energy at 0.6000 = -20886.389789 +Energy at 0.6667 = -20771.132766 +Energy at 0.7333 = -20673.343195 +Energy at 0.8000 = -20598.884140 +Energy at 0.8667 = -20551.509761 +Energy at 0.9333 = -20530.475966 +Energy at 1.0000 = -20527.018427 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 299.11 PRESS =******** + Etot = -17729.5249 EKtot = 3848.1375 EPtot = -21577.6625 + BOND = 8.1288 ANGLE = 104.5238 DIHED = 4.3669 + 1-4 NB = 4.9543 1-4 EEL = -33.5151 VDWAALS = 3094.9338 + EELEC = -24762.7269 EHBOND = 0.0000 RESTRAINT = 1.6720 + EAMBER (non-restraint) = -21579.3344 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65483.6402 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9431 SC_EKtot= 0.0000 SC_EPtot = 0.9431 + SC_BOND= 0.0000 SC_ANGLE= 0.9419 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 200 TIME(PS) = 0.400 TEMP(K) = 299.11 PRESS = 0.0 + Etot = -17729.5249 EKtot = 3848.1375 EPtot = -21577.6625 + BOND = 8.1288 ANGLE = 104.5238 DIHED = 4.3669 + 1-4 NB = 4.9543 1-4 EEL = -33.5151 VDWAALS = 3094.9338 + EELEC = -24762.7269 EHBOND = 0.0000 RESTRAINT = 1.6720 + EAMBER (non-restraint) = -21579.3344 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65483.6402 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9431 SC_EKtot= 0.0000 SC_EPtot = 0.9431 + SC_BOND= 0.0000 SC_ANGLE= 0.9419 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -3.78774 1.00000 0.00000 -0.00000 +TI 2 vDW -4.22919 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -3.7877 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.12877 1.00000 0.00000 -0.00000 +TI 2 Bond 424.96864 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.1288 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 104.52381 1.00000 0.00000 -0.00000 +TI 2 Angle 221.53412 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 104.5238 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.36687 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.81268 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.3669 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.51509 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.51509 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.5151 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 4.95429 1.00000 0.00000 -0.00000 +TI 2 VDW14 4.88198 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 4.9543 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 223.62019 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 447.61572 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 223.6202 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -108.96675 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 31.01459 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -108.9668 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 180.59123 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.72422 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02504 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01409 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21439.240358 +Energy at 0.0667 = -21436.569044 +Energy at 0.1333 = -21420.047126 +Energy at 0.2000 = -21381.348536 +Energy at 0.2667 = -21317.294906 +Energy at 0.3333 = -21228.898916 +Energy at 0.4000 = -21120.365162 +Energy at 0.4667 = -20998.249282 +Energy at 0.5333 = -20870.529218 +Energy at 0.6000 = -20745.673330 +Energy at 0.6667 = -20631.944284 +Energy at 0.7333 = -20536.599769 +Energy at 0.8000 = -20465.163662 +Energy at 0.8667 = -20420.532635 +Energy at 0.9333 = -20401.003846 +Energy at 1.0000 = -20397.814094 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 289.77 PRESS = 0.0 + Etot = -17711.2914 EKtot = 3727.9490 EPtot = -21439.2404 + BOND = 6.9047 ANGLE = 106.8872 DIHED = 4.6870 + 1-4 NB = 6.2270 1-4 EEL = -33.8221 VDWAALS = 2992.4854 + EELEC = -24524.7962 EHBOND = 0.0000 RESTRAINT = 2.1867 + EAMBER (non-restraint) = -21441.4271 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65483.6402 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.3105 SC_EKtot= 0.0000 SC_EPtot = 1.3105 + SC_BOND= 0.0000 SC_ANGLE= 1.3093 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 400 TIME(PS) = 0.800 TEMP(K) = 289.77 PRESS = 0.0 + Etot = -17711.2914 EKtot = 3727.9490 EPtot = -21439.2404 + BOND = 6.9047 ANGLE = 106.8872 DIHED = 4.6870 + 1-4 NB = 6.2270 1-4 EEL = -33.8221 VDWAALS = 2992.4854 + EELEC = -24524.7962 EHBOND = 0.0000 RESTRAINT = 2.1867 + EAMBER (non-restraint) = -21441.4271 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65483.6402 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.3105 SC_EKtot= 0.0000 SC_EPtot = 1.3105 + SC_BOND= 0.0000 SC_ANGLE= 1.3093 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -8.38790 1.00000 0.00000 -0.00000 +TI 2 vDW -8.80211 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -8.3879 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.90466 1.00000 0.00000 -0.00000 +TI 2 Bond 372.16983 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.9047 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 106.88716 1.00000 0.00000 -0.00000 +TI 2 Angle 231.91791 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 106.8872 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.68699 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.49596 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.6870 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.82209 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.82209 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.8221 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.22705 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.15702 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.2270 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 222.14294 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 491.71686 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 222.1429 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -105.98516 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 49.38881 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -105.9852 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 171.58531 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.99742 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02487 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0249 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01400 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21537.682347 +Energy at 0.0667 = -21534.670490 +Energy at 0.1333 = -21516.042457 +Energy at 0.2000 = -21472.411707 +Energy at 0.2667 = -21400.197543 +Energy at 0.3333 = -21300.547867 +Energy at 0.4000 = -21178.215470 +Energy at 0.4667 = -21040.616950 +Energy at 0.5333 = -20896.800753 +Energy at 0.6000 = -20756.421596 +Energy at 0.6667 = -20628.973879 +Energy at 0.7333 = -20522.836509 +Energy at 0.8000 = -20444.216791 +Energy at 0.8667 = -20395.826047 +Energy at 0.9333 = -20374.920894 +Energy at 1.0000 = -20371.525694 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 600 TIME(PS) = 1.200 TEMP(K) = 299.61 PRESS = 0.0 + Etot = -17683.1326 EKtot = 3854.5497 EPtot = -21537.6823 + BOND = 7.4462 ANGLE = 101.3144 DIHED = 3.5441 + 1-4 NB = 7.4910 1-4 EEL = -33.9679 VDWAALS = 3115.5266 + EELEC = -24743.2707 EHBOND = 0.0000 RESTRAINT = 4.2340 + EAMBER (non-restraint) = -21541.9164 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65483.6402 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6102 SC_EKtot= 0.0000 SC_EPtot = 0.6102 + SC_BOND= 0.0000 SC_ANGLE= 0.6090 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 600 TIME(PS) = 1.200 TEMP(K) = 299.61 PRESS = 0.0 + Etot = -17683.1326 EKtot = 3854.5497 EPtot = -21537.6823 + BOND = 7.4462 ANGLE = 101.3144 DIHED = 3.5441 + 1-4 NB = 7.4910 1-4 EEL = -33.9679 VDWAALS = 3115.5266 + EELEC = -24743.2707 EHBOND = 0.0000 RESTRAINT = 4.2340 + EAMBER (non-restraint) = -21541.9164 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65483.6402 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6102 SC_EKtot= 0.0000 SC_EPtot = 0.6102 + SC_BOND= 0.0000 SC_ANGLE= 0.6090 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW 8.28748 1.00000 0.00000 -0.00000 +TI 2 vDW 7.85305 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= 8.2875 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 7.44616 1.00000 0.00000 -0.00000 +TI 2 Bond 511.47566 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 7.4462 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.31441 1.00000 0.00000 -0.00000 +TI 2 Angle 227.07543 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.3144 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 3.54408 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.16326 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 3.5441 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.96791 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.96791 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.9679 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 7.49104 1.00000 0.00000 -0.00000 +TI 2 VDW14 7.41389 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 7.4910 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 229.30705 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 466.86996 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 229.3071 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -120.75315 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 53.10169 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -120.7532 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 172.88460 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.74022 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02515 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0251 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01415 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21575.288851 +Energy at 0.0667 = -21572.577471 +Energy at 0.1333 = -21555.807646 +Energy at 0.2000 = -21516.527754 +Energy at 0.2667 = -21451.509943 +Energy at 0.3333 = -21361.779403 +Energy at 0.4000 = -21251.602644 +Energy at 0.4667 = -21127.641144 +Energy at 0.5333 = -20998.024577 +Energy at 0.6000 = -20871.431998 +Energy at 0.6667 = -20756.410211 +Energy at 0.7333 = -20660.526089 +Energy at 0.8000 = -20589.423850 +Energy at 0.8667 = -20545.617785 +Energy at 0.9333 = -20526.681524 +Energy at 1.0000 = -20523.605373 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 800 TIME(PS) = 1.600 TEMP(K) = 299.47 PRESS = 0.0 + Etot = -17722.6422 EKtot = 3852.6466 EPtot = -21575.2889 + BOND = 4.9038 ANGLE = 99.0835 DIHED = 5.0587 + 1-4 NB = 7.7230 1-4 EEL = -34.1915 VDWAALS = 3116.6282 + EELEC = -24776.1092 EHBOND = 0.0000 RESTRAINT = 1.6146 + EAMBER (non-restraint) = -21576.9034 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65208.5899 + Density = 0.9972 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6131 SC_EKtot= 0.0000 SC_EPtot = 0.6131 + SC_BOND= 0.0000 SC_ANGLE= 0.6119 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 800 TIME(PS) = 1.600 TEMP(K) = 299.47 PRESS = 0.0 + Etot = -17722.6422 EKtot = 3852.6466 EPtot = -21575.2889 + BOND = 4.9038 ANGLE = 99.0835 DIHED = 5.0587 + 1-4 NB = 7.7230 1-4 EEL = -34.1915 VDWAALS = 3116.6282 + EELEC = -24776.1092 EHBOND = 0.0000 RESTRAINT = 1.6146 + EAMBER (non-restraint) = -21576.9034 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65208.5899 + Density = 0.9972 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6131 SC_EKtot= 0.0000 SC_EPtot = 0.6131 + SC_BOND= 0.0000 SC_ANGLE= 0.6119 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -3.19689 1.00000 0.00000 -0.00000 +TI 2 vDW -3.62927 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -3.1969 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 4.90379 1.00000 0.00000 -0.00000 +TI 2 Bond 454.66375 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 4.9038 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.08354 1.00000 0.00000 -0.00000 +TI 2 Angle 229.15761 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.0835 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.05874 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.13801 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.0587 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.19149 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.19149 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.1915 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 7.72301 1.00000 0.00000 -0.00000 +TI 2 VDW14 7.64899 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 7.7230 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 219.26328 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 452.61542 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 219.2633 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -87.33041 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 31.33487 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -87.3304 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 171.06729 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.35824 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02527 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01422 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21551.534399 +Energy at 0.0667 = -21548.736211 +Energy at 0.1333 = -21531.429028 +Energy at 0.2000 = -21490.887367 +Energy at 0.2667 = -21423.770951 +Energy at 0.3333 = -21331.121804 +Energy at 0.4000 = -21217.321593 +Energy at 0.4667 = -21089.222121 +Energy at 0.5333 = -20955.195026 +Energy at 0.6000 = -20824.191537 +Energy at 0.6667 = -20705.048904 +Energy at 0.7333 = -20605.623326 +Energy at 0.8000 = -20531.815077 +Energy at 0.8667 = -20486.299839 +Energy at 0.9333 = -20466.613129 +Energy at 1.0000 = -20463.414345 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 302.90 PRESS = 0.0 + Etot = -17654.6563 EKtot = 3896.8781 EPtot = -21551.5344 + BOND = 7.0639 ANGLE = 101.2149 DIHED = 5.1798 + 1-4 NB = 6.2916 1-4 EEL = -32.5264 VDWAALS = 3100.5103 + EELEC = -24740.8102 EHBOND = 0.0000 RESTRAINT = 1.5416 + EAMBER (non-restraint) = -21553.0760 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65186.3948 + Density = 0.9975 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7747 SC_EKtot= 0.0000 SC_EPtot = 0.7747 + SC_BOND= 0.0000 SC_ANGLE= 0.7735 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 302.90 PRESS = 0.0 + Etot = -17654.6563 EKtot = 3896.8781 EPtot = -21551.5344 + BOND = 7.0639 ANGLE = 101.2149 DIHED = 5.1798 + 1-4 NB = 6.2916 1-4 EEL = -32.5264 VDWAALS = 3100.5103 + EELEC = -24740.8102 EHBOND = 0.0000 RESTRAINT = 1.5416 + EAMBER (non-restraint) = -21553.0760 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65186.3948 + Density = 0.9975 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 1 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7747 SC_EKtot= 0.0000 SC_EPtot = 0.7747 + SC_BOND= 0.0000 SC_ANGLE= 0.7735 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -2.91604 1.00000 0.00000 -0.00000 +TI 2 vDW -3.32517 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -2.9160 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 7.06392 1.00000 0.00000 -0.00000 +TI 2 Bond 446.83586 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 7.0639 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.21489 1.00000 0.00000 -0.00000 +TI 2 Angle 225.66711 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.2149 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.17976 1.00000 0.00000 -0.00000 +TI 2 Torsion 9.11684 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.1798 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.52635 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.52635 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.5264 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.29162 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.22418 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.2916 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 210.39702 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 448.83118 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 210.3970 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -113.63854 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 40.14542 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -113.6385 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 172.74570 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.06803 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02516 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01416 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21538.493318 +Energy at 0.0667 = -21535.676409 +Energy at 0.1333 = -21518.253474 +Energy at 0.2000 = -21477.440854 +Energy at 0.2667 = -21409.875832 +Energy at 0.3333 = -21316.604697 +Energy at 0.4000 = -21202.027527 +Energy at 0.4667 = -21073.012846 +Energy at 0.5333 = -20937.926751 +Energy at 0.6000 = -20805.673935 +Energy at 0.6667 = -20685.011124 +Energy at 0.7333 = -20583.754615 +Energy at 0.8000 = -20507.969193 +Energy at 0.8667 = -20460.799338 +Energy at 0.9333 = -20440.251475 +Energy at 1.0000 = -20436.902827 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 1200 TIME(PS) = 2.400 TEMP(K) = 300.71 PRESS = 0.0 + Etot = -17669.8179 EKtot = 3868.6754 EPtot = -21538.4933 + BOND = 11.3589 ANGLE = 99.6080 DIHED = 3.9954 + 1-4 NB = 5.3977 1-4 EEL = -33.7170 VDWAALS = 3146.5122 + EELEC = -24775.8538 EHBOND = 0.0000 RESTRAINT = 4.2053 + EAMBER (non-restraint) = -21542.6986 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65186.3948 + Density = 0.9975 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7628 SC_EKtot= 0.0000 SC_EPtot = 0.7628 + SC_BOND= 0.0000 SC_ANGLE= 0.7616 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 1200 TIME(PS) = 2.400 TEMP(K) = 300.71 PRESS = 0.0 + Etot = -17669.8179 EKtot = 3868.6754 EPtot = -21538.4933 + BOND = 11.3589 ANGLE = 99.6080 DIHED = 3.9954 + 1-4 NB = 5.3977 1-4 EEL = -33.7170 VDWAALS = 3146.5122 + EELEC = -24775.8538 EHBOND = 0.0000 RESTRAINT = 4.2053 + EAMBER (non-restraint) = -21542.6986 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65186.3948 + Density = 0.9975 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7628 SC_EKtot= 0.0000 SC_EPtot = 0.7628 + SC_BOND= 0.0000 SC_ANGLE= 0.7616 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -4.37670 1.00000 0.00000 -0.00000 +TI 2 vDW -4.78982 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -4.3767 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 11.35886 1.00000 0.00000 -0.00000 +TI 2 Bond 484.60788 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 11.3589 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.60800 1.00000 0.00000 -0.00000 +TI 2 Angle 220.75597 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.6080 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 3.99545 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.83468 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 3.9954 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.71700 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.71700 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.7170 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.39771 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.33299 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.3977 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 212.59796 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 455.54211 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 212.5980 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -93.94371 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 36.10747 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -93.9437 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 172.91529 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.08980 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02498 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01406 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21527.499149 +Energy at 0.0667 = -21524.873869 +Energy at 0.1333 = -21508.637686 +Energy at 0.2000 = -21470.615541 +Energy at 0.2667 = -21407.705572 +Energy at 0.3333 = -21320.944570 +Energy at 0.4000 = -21214.529915 +Energy at 0.4667 = -21094.997398 +Energy at 0.5333 = -20970.314892 +Energy at 0.6000 = -20848.971125 +Energy at 0.6667 = -20739.267675 +Energy at 0.7333 = -20648.419133 +Energy at 0.8000 = -20581.569442 +Energy at 0.8667 = -20540.684389 +Energy at 0.9333 = -20523.098829 +Energy at 1.0000 = -20520.247698 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 1400 TIME(PS) = 2.800 TEMP(K) = 301.83 PRESS = 0.0 + Etot = -17644.4416 EKtot = 3883.0576 EPtot = -21527.4991 + BOND = 10.0163 ANGLE = 102.0610 DIHED = 2.2840 + 1-4 NB = 5.4515 1-4 EEL = -33.1940 VDWAALS = 3039.4219 + EELEC = -24656.0076 EHBOND = 0.0000 RESTRAINT = 2.4676 + EAMBER (non-restraint) = -21529.9668 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65093.4091 + Density = 0.9989 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3049 SC_EKtot= 0.0000 SC_EPtot = 0.3049 + SC_BOND= 0.0000 SC_ANGLE= 0.3037 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 1400 TIME(PS) = 2.800 TEMP(K) = 301.83 PRESS = 0.0 + Etot = -17644.4416 EKtot = 3883.0576 EPtot = -21527.4991 + BOND = 10.0163 ANGLE = 102.0610 DIHED = 2.2840 + 1-4 NB = 5.4515 1-4 EEL = -33.1940 VDWAALS = 3039.4219 + EELEC = -24656.0076 EHBOND = 0.0000 RESTRAINT = 2.4676 + EAMBER (non-restraint) = -21529.9668 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65093.4091 + Density = 0.9989 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3049 SC_EKtot= 0.0000 SC_EPtot = 0.3049 + SC_BOND= 0.0000 SC_ANGLE= 0.3037 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -12.15582 1.00000 0.00000 -0.00000 +TI 2 vDW -12.48718 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -12.1558 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 10.01631 1.00000 0.00000 -0.00000 +TI 2 Bond 432.92888 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 10.0163 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 102.06098 1.00000 0.00000 -0.00000 +TI 2 Angle 231.59968 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 102.0610 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 2.28401 1.00000 0.00000 -0.00000 +TI 2 Torsion 2.30938 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 2.2840 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.19395 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.19395 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.1940 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.45154 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.37681 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.4515 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 211.18890 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 437.47467 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 211.1889 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -85.74426 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 44.38539 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -85.7443 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 162.80250 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -48.33181 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02507 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0251 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01411 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21516.923090 +Energy at 0.0667 = -21514.145488 +Energy at 0.1333 = -21496.965978 +Energy at 0.2000 = -21456.725646 +Energy at 0.2667 = -21390.114938 +Energy at 0.3333 = -21298.177198 +Energy at 0.4000 = -21185.268338 +Energy at 0.4667 = -21058.182372 +Energy at 0.5333 = -20925.189688 +Energy at 0.6000 = -20795.081759 +Energy at 0.6667 = -20676.477533 +Energy at 0.7333 = -20577.026909 +Energy at 0.8000 = -20502.623450 +Energy at 0.8667 = -20456.307667 +Energy at 0.9333 = -20436.124141 +Energy at 1.0000 = -20432.834152 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 1600 TIME(PS) = 3.200 TEMP(K) = 300.59 PRESS = 0.0 + Etot = -17649.8654 EKtot = 3867.0576 EPtot = -21516.9231 + BOND = 9.4456 ANGLE = 100.7330 DIHED = 5.1713 + 1-4 NB = 5.4283 1-4 EEL = -33.7877 VDWAALS = 3048.6692 + EELEC = -24655.5685 EHBOND = 0.0000 RESTRAINT = 2.9857 + EAMBER (non-restraint) = -21519.9088 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65086.0435 + Density = 0.9990 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.2421 SC_EKtot= 0.0000 SC_EPtot = 1.2421 + SC_BOND= 0.0000 SC_ANGLE= 1.2409 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 1600 TIME(PS) = 3.200 TEMP(K) = 300.59 PRESS = 0.0 + Etot = -17649.8654 EKtot = 3867.0576 EPtot = -21516.9231 + BOND = 9.4456 ANGLE = 100.7330 DIHED = 5.1713 + 1-4 NB = 5.4283 1-4 EEL = -33.7877 VDWAALS = 3048.6692 + EELEC = -24655.5685 EHBOND = 0.0000 RESTRAINT = 2.9857 + EAMBER (non-restraint) = -21519.9088 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65086.0435 + Density = 0.9990 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.2421 SC_EKtot= 0.0000 SC_EPtot = 1.2421 + SC_BOND= 0.0000 SC_ANGLE= 1.2409 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -5.22684 1.00000 0.00000 -0.00000 +TI 2 vDW -5.60827 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -5.2268 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 9.44557 1.00000 0.00000 -0.00000 +TI 2 Bond 443.54133 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 9.4456 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.73303 1.00000 0.00000 -0.00000 +TI 2 Angle 215.52421 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.7330 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.17130 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.96927 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.1713 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.78769 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.78769 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.7877 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.42832 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.35789 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.4283 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 208.64992 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 470.22202 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 208.6499 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -100.90094 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 44.72128 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -100.9009 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 171.72771 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.26782 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02520 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01418 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21552.278540 +Energy at 0.0667 = -21549.356191 +Energy at 0.1333 = -21531.282689 +Energy at 0.2000 = -21488.957338 +Energy at 0.2667 = -21418.925766 +Energy at 0.3333 = -21322.339620 +Energy at 0.4000 = -21203.868091 +Energy at 0.4667 = -21070.782636 +Energy at 0.5333 = -20931.946786 +Energy at 0.6000 = -20796.799332 +Energy at 0.6667 = -20674.565810 +Energy at 0.7333 = -20573.266442 +Energy at 0.8000 = -20498.645101 +Energy at 0.8667 = -20452.950551 +Energy at 0.9333 = -20433.277950 +Energy at 1.0000 = -20430.087218 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 1800 TIME(PS) = 3.600 TEMP(K) = 299.35 PRESS = 0.0 + Etot = -17701.1797 EKtot = 3851.0988 EPtot = -21552.2785 + BOND = 7.2248 ANGLE = 101.7487 DIHED = 3.9569 + 1-4 NB = 5.7999 1-4 EEL = -32.3371 VDWAALS = 3103.8524 + EELEC = -24744.0701 EHBOND = 0.0000 RESTRAINT = 1.5460 + EAMBER (non-restraint) = -21553.8246 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64805.3903 + Density = 1.0034 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6848 SC_EKtot= 0.0000 SC_EPtot = 0.6848 + SC_BOND= 0.0000 SC_ANGLE= 0.6836 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 1800 TIME(PS) = 3.600 TEMP(K) = 299.35 PRESS = 0.0 + Etot = -17701.1797 EKtot = 3851.0988 EPtot = -21552.2785 + BOND = 7.2248 ANGLE = 101.7487 DIHED = 3.9569 + 1-4 NB = 5.7999 1-4 EEL = -32.3371 VDWAALS = 3103.8524 + EELEC = -24744.0701 EHBOND = 0.0000 RESTRAINT = 1.5460 + EAMBER (non-restraint) = -21553.8246 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64805.3903 + Density = 1.0034 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6848 SC_EKtot= 0.0000 SC_EPtot = 0.6848 + SC_BOND= 0.0000 SC_ANGLE= 0.6836 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -9.58130 1.00000 0.00000 -0.00000 +TI 2 vDW -9.97376 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -9.5813 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 7.22476 1.00000 0.00000 -0.00000 +TI 2 Bond 522.11270 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 7.2248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.74874 1.00000 0.00000 -0.00000 +TI 2 Angle 217.07703 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.7487 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 3.95686 1.00000 0.00000 -0.00000 +TI 2 Torsion 6.90177 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 3.9569 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.33712 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.33712 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.3371 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.79992 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.73439 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.7999 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 213.23399 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 462.46191 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 213.2340 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -92.96726 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 40.81138 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -92.9673 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 163.10466 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -44.80645 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02548 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0255 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01434 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21595.562614 +Energy at 0.0667 = -21592.675576 +Energy at 0.1333 = -21574.818732 +Energy at 0.2000 = -21532.988599 +Energy at 0.2667 = -21463.735455 +Energy at 0.3333 = -21368.125515 +Energy at 0.4000 = -21250.659595 +Energy at 0.4667 = -21118.367173 +Energy at 0.5333 = -20979.814625 +Energy at 0.6000 = -20844.127555 +Energy at 0.6667 = -20720.292401 +Energy at 0.7333 = -20616.343579 +Energy at 0.8000 = -20538.522380 +Energy at 0.8667 = -20490.071304 +Energy at 0.9333 = -20468.959512 +Energy at 1.0000 = -20465.518488 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 297.41 PRESS = 0.0 + Etot = -17769.3084 EKtot = 3826.2542 EPtot = -21595.5626 + BOND = 3.6285 ANGLE = 101.3073 DIHED = 8.5825 + 1-4 NB = 5.9997 1-4 EEL = -35.3531 VDWAALS = 3062.6110 + EELEC = -24745.7865 EHBOND = 0.0000 RESTRAINT = 3.4479 + EAMBER (non-restraint) = -21599.0105 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64911.5685 + Density = 1.0017 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.5064 SC_EKtot= 0.0000 SC_EPtot = 0.5064 + SC_BOND= 0.0000 SC_ANGLE= 0.5052 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 2000 TIME(PS) = 4.000 TEMP(K) = 297.41 PRESS = 0.0 + Etot = -17769.3084 EKtot = 3826.2542 EPtot = -21595.5626 + BOND = 3.6285 ANGLE = 101.3073 DIHED = 8.5825 + 1-4 NB = 5.9997 1-4 EEL = -35.3531 VDWAALS = 3062.6110 + EELEC = -24745.7865 EHBOND = 0.0000 RESTRAINT = 3.4479 + EAMBER (non-restraint) = -21599.0105 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64911.5685 + Density = 1.0017 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 2 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.5064 SC_EKtot= 0.0000 SC_EPtot = 0.5064 + SC_BOND= 0.0000 SC_ANGLE= 0.5052 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -5.46802 1.00000 0.00000 -0.00000 +TI 2 vDW -5.94575 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -5.4680 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 3.62854 1.00000 0.00000 -0.00000 +TI 2 Bond 462.31971 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 3.6285 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.30729 1.00000 0.00000 -0.00000 +TI 2 Angle 222.50306 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.3073 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 8.58255 1.00000 0.00000 -0.00000 +TI 2 Torsion 8.99247 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 8.5825 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -35.35315 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -35.35315 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -35.3531 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.99972 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.92800 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.9997 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 206.86748 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 475.59982 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 206.8675 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -102.83293 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 39.83411 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -102.8329 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 177.83947 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -48.19300 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02526 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01422 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21583.716175 +Energy at 0.0667 = -21580.913368 +Energy at 0.1333 = -21563.578601 +Energy at 0.2000 = -21522.979124 +Energy at 0.2667 = -21455.788829 +Energy at 0.3333 = -21363.085471 +Energy at 0.4000 = -21249.301169 +Energy at 0.4667 = -21121.338328 +Energy at 0.5333 = -20987.596120 +Energy at 0.6000 = -20857.001282 +Energy at 0.6667 = -20738.292864 +Energy at 0.7333 = -20639.176337 +Energy at 0.8000 = -20565.447553 +Energy at 0.8667 = -20519.840621 +Energy at 0.9333 = -20500.061460 +Energy at 1.0000 = -20496.843889 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 2200 TIME(PS) = 4.400 TEMP(K) = 296.18 PRESS = 0.0 + Etot = -17773.3500 EKtot = 3810.3662 EPtot = -21583.7162 + BOND = 4.7516 ANGLE = 95.7603 DIHED = 7.8817 + 1-4 NB = 5.3170 1-4 EEL = -33.3044 VDWAALS = 3193.0183 + EELEC = -24860.1339 EHBOND = 0.0000 RESTRAINT = 2.9931 + EAMBER (non-restraint) = -21586.7093 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64744.5981 + Density = 1.0043 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.0684 SC_EKtot= 0.0000 SC_EPtot = 1.0684 + SC_BOND= 0.0000 SC_ANGLE= 1.0672 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 2200 TIME(PS) = 4.400 TEMP(K) = 296.18 PRESS = 0.0 + Etot = -17773.3500 EKtot = 3810.3662 EPtot = -21583.7162 + BOND = 4.7516 ANGLE = 95.7603 DIHED = 7.8817 + 1-4 NB = 5.3170 1-4 EEL = -33.3044 VDWAALS = 3193.0183 + EELEC = -24860.1339 EHBOND = 0.0000 RESTRAINT = 2.9931 + EAMBER (non-restraint) = -21586.7093 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64744.5981 + Density = 1.0043 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.0684 SC_EKtot= 0.0000 SC_EPtot = 1.0684 + SC_BOND= 0.0000 SC_ANGLE= 1.0672 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -7.44090 1.00000 0.00000 -0.00000 +TI 2 vDW -7.83425 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -7.4409 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 4.75164 1.00000 0.00000 -0.00000 +TI 2 Bond 449.67474 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 4.7516 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 95.76030 1.00000 0.00000 -0.00000 +TI 2 Angle 213.79984 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 95.7603 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 7.88172 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.57522 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 7.8817 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.30442 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.30442 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.3044 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.31702 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.24849 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.3170 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 210.42389 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 457.13254 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 210.4239 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -102.83869 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 60.54048 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -102.8387 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 165.01410 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.98070 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02533 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01426 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21633.126034 +Energy at 0.0667 = -21630.187046 +Energy at 0.1333 = -21612.009090 +Energy at 0.2000 = -21569.428127 +Energy at 0.2667 = -21498.935832 +Energy at 0.3333 = -21401.621269 +Energy at 0.4000 = -21282.063337 +Energy at 0.4667 = -21147.393901 +Energy at 0.5333 = -21006.263228 +Energy at 0.6000 = -20867.813829 +Energy at 0.6667 = -20740.963091 +Energy at 0.7333 = -20633.673460 +Energy at 0.8000 = -20552.377650 +Energy at 0.8667 = -20501.025645 +Energy at 0.9333 = -20478.390310 +Energy at 1.0000 = -20474.682743 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 2400 TIME(PS) = 4.800 TEMP(K) = 303.07 PRESS = 0.0 + Etot = -17734.0739 EKtot = 3899.0521 EPtot = -21633.1260 + BOND = 5.3778 ANGLE = 98.6604 DIHED = 2.7203 + 1-4 NB = 6.6364 1-4 EEL = -33.2961 VDWAALS = 3216.4189 + EELEC = -24930.4599 EHBOND = 0.0000 RESTRAINT = 0.8161 + EAMBER (non-restraint) = -21633.9422 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64744.5981 + Density = 1.0043 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.3033 SC_EKtot= 0.0000 SC_EPtot = 1.3033 + SC_BOND= 0.0000 SC_ANGLE= 1.3020 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 2400 TIME(PS) = 4.800 TEMP(K) = 303.07 PRESS = 0.0 + Etot = -17734.0739 EKtot = 3899.0521 EPtot = -21633.1260 + BOND = 5.3778 ANGLE = 98.6604 DIHED = 2.7203 + 1-4 NB = 6.6364 1-4 EEL = -33.2961 VDWAALS = 3216.4189 + EELEC = -24930.4599 EHBOND = 0.0000 RESTRAINT = 0.8161 + EAMBER (non-restraint) = -21633.9422 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64744.5981 + Density = 1.0043 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.3033 SC_EKtot= 0.0000 SC_EPtot = 1.3033 + SC_BOND= 0.0000 SC_ANGLE= 1.3020 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -2.35547 1.00000 0.00000 -0.00000 +TI 2 vDW -2.79164 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -2.3555 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.37775 1.00000 0.00000 -0.00000 +TI 2 Bond 489.96269 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.3778 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 98.66039 1.00000 0.00000 -0.00000 +TI 2 Angle 231.70125 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 98.6604 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 2.72029 1.00000 0.00000 -0.00000 +TI 2 Torsion 2.67937 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 2.7203 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.29609 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.29609 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.2961 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.63644 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.57080 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.6364 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 214.03516 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 448.11569 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 214.0352 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -113.19879 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 49.25867 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -113.1988 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 172.26229 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.66819 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02537 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0254 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01428 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21685.659652 +Energy at 0.0667 = -21683.031389 +Energy at 0.1333 = -21666.775271 +Energy at 0.2000 = -21628.695987 +Energy at 0.2667 = -21565.656693 +Energy at 0.3333 = -21478.636212 +Energy at 0.4000 = -21371.747601 +Energy at 0.4667 = -21251.417783 +Energy at 0.5333 = -21125.490103 +Energy at 0.6000 = -21002.337504 +Energy at 0.6667 = -20890.216294 +Energy at 0.7333 = -20796.479513 +Energy at 0.8000 = -20726.713241 +Energy at 0.8667 = -20683.568303 +Energy at 0.9333 = -20664.867482 +Energy at 1.0000 = -20661.826259 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 2600 TIME(PS) = 5.200 TEMP(K) = 302.48 PRESS = 0.0 + Etot = -17794.2724 EKtot = 3891.3873 EPtot = -21685.6597 + BOND = 9.1312 ANGLE = 105.6284 DIHED = 5.3130 + 1-4 NB = 4.9069 1-4 EEL = -34.0787 VDWAALS = 3156.6604 + EELEC = -24935.2137 EHBOND = 0.0000 RESTRAINT = 1.9929 + EAMBER (non-restraint) = -21687.6526 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64712.8592 + Density = 1.0048 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.2150 SC_EKtot= 0.0000 SC_EPtot = 1.2150 + SC_BOND= 0.0000 SC_ANGLE= 1.2138 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 2600 TIME(PS) = 5.200 TEMP(K) = 302.48 PRESS = 0.0 + Etot = -17794.2724 EKtot = 3891.3873 EPtot = -21685.6597 + BOND = 9.1312 ANGLE = 105.6284 DIHED = 5.3130 + 1-4 NB = 4.9069 1-4 EEL = -34.0787 VDWAALS = 3156.6604 + EELEC = -24935.2137 EHBOND = 0.0000 RESTRAINT = 1.9929 + EAMBER (non-restraint) = -21687.6526 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64712.8592 + Density = 1.0048 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.2150 SC_EKtot= 0.0000 SC_EPtot = 1.2150 + SC_BOND= 0.0000 SC_ANGLE= 1.2138 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -4.10505 1.00000 0.00000 -0.00000 +TI 2 vDW -4.54962 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -4.1051 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 9.13119 1.00000 0.00000 -0.00000 +TI 2 Bond 398.82299 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 9.1312 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 105.62843 1.00000 0.00000 -0.00000 +TI 2 Angle 227.67583 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 105.6284 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.31297 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.19580 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.3130 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.07872 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.07872 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.0787 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 4.90692 1.00000 0.00000 -0.00000 +TI 2 VDW14 4.83655 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 4.9069 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 214.29971 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 457.26840 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 214.2997 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -100.17395 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 43.86553 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -100.1740 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 173.63082 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.68732 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02534 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01426 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21621.426877 +Energy at 0.0667 = -21618.606243 +Energy at 0.1333 = -21601.160977 +Energy at 0.2000 = -21560.301078 +Energy at 0.2667 = -21492.675011 +Energy at 0.3333 = -21399.361744 +Energy at 0.4000 = -21284.819508 +Energy at 0.4667 = -21156.005712 +Energy at 0.5333 = -21021.411317 +Energy at 0.6000 = -20890.099031 +Energy at 0.6667 = -20770.978203 +Energy at 0.7333 = -20671.893153 +Energy at 0.8000 = -20598.610494 +Energy at 0.8667 = -20553.576844 +Energy at 0.9333 = -20534.144526 +Energy at 1.0000 = -20530.990016 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 2800 TIME(PS) = 5.600 TEMP(K) = 298.87 PRESS = 0.0 + Etot = -17776.4759 EKtot = 3844.9510 EPtot = -21621.4269 + BOND = 8.9892 ANGLE = 99.0833 DIHED = 6.5490 + 1-4 NB = 6.3154 1-4 EEL = -32.8328 VDWAALS = 2968.0103 + EELEC = -24679.5142 EHBOND = 0.0000 RESTRAINT = 1.9731 + EAMBER (non-restraint) = -21623.4000 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64940.6571 + Density = 1.0013 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.1518 SC_EKtot= 0.0000 SC_EPtot = 1.1518 + SC_BOND= 0.0000 SC_ANGLE= 1.1506 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 2800 TIME(PS) = 5.600 TEMP(K) = 298.87 PRESS = 0.0 + Etot = -17776.4759 EKtot = 3844.9510 EPtot = -21621.4269 + BOND = 8.9892 ANGLE = 99.0833 DIHED = 6.5490 + 1-4 NB = 6.3154 1-4 EEL = -32.8328 VDWAALS = 2968.0103 + EELEC = -24679.5142 EHBOND = 0.0000 RESTRAINT = 1.9731 + EAMBER (non-restraint) = -21623.4000 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64940.6571 + Density = 1.0013 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.1518 SC_EKtot= 0.0000 SC_EPtot = 1.1518 + SC_BOND= 0.0000 SC_ANGLE= 1.1506 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -10.68483 1.00000 0.00000 -0.00000 +TI 2 vDW -11.08784 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -10.6848 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.98916 1.00000 0.00000 -0.00000 +TI 2 Bond 471.22509 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.9892 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.08326 1.00000 0.00000 -0.00000 +TI 2 Angle 210.52655 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.0833 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.54896 1.00000 0.00000 -0.00000 +TI 2 Torsion 6.31265 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.5490 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.83279 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.83279 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.8328 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.31538 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.24259 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.3154 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 226.57144 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 477.66034 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 226.5714 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -103.23939 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 44.89080 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -103.2394 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 170.38751 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.59619 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02525 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01421 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21613.108668 +Energy at 0.0667 = -21610.399905 +Energy at 0.1333 = -21593.646218 +Energy at 0.2000 = -21554.403740 +Energy at 0.2667 = -21489.446389 +Energy at 0.3333 = -21399.795042 +Energy at 0.4000 = -21289.704642 +Energy at 0.4667 = -21165.814377 +Energy at 0.5333 = -21036.214356 +Energy at 0.6000 = -20909.518108 +Energy at 0.6667 = -20794.180022 +Energy at 0.7333 = -20697.684042 +Energy at 0.8000 = -20625.711235 +Energy at 0.8667 = -20581.049378 +Energy at 0.9333 = -20561.629334 +Energy at 1.0000 = -20558.466517 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 300.24 PRESS = 0.0 + Etot = -17750.5336 EKtot = 3862.5751 EPtot = -21613.1087 + BOND = 5.1247 ANGLE = 99.6879 DIHED = 3.3247 + 1-4 NB = 6.3209 1-4 EEL = -31.4955 VDWAALS = 3148.2820 + EELEC = -24846.3180 EHBOND = 0.0000 RESTRAINT = 1.9647 + EAMBER (non-restraint) = -21615.0734 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64940.6571 + Density = 1.0013 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3913 SC_EKtot= 0.0000 SC_EPtot = 0.3913 + SC_BOND= 0.0000 SC_ANGLE= 0.3901 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 3000 TIME(PS) = 6.000 TEMP(K) = 300.24 PRESS = 0.0 + Etot = -17750.5336 EKtot = 3862.5751 EPtot = -21613.1087 + BOND = 5.1247 ANGLE = 99.6879 DIHED = 3.3247 + 1-4 NB = 6.3209 1-4 EEL = -31.4955 VDWAALS = 3148.2820 + EELEC = -24846.3180 EHBOND = 0.0000 RESTRAINT = 1.9647 + EAMBER (non-restraint) = -21615.0734 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64940.6571 + Density = 1.0013 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 3 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3913 SC_EKtot= 0.0000 SC_EPtot = 0.3913 + SC_BOND= 0.0000 SC_ANGLE= 0.3901 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -3.18111 1.00000 0.00000 -0.00000 +TI 2 vDW -3.62224 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -3.1811 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.12473 1.00000 0.00000 -0.00000 +TI 2 Bond 409.53364 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.1247 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.68785 1.00000 0.00000 -0.00000 +TI 2 Angle 216.57097 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.6879 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 3.32466 1.00000 0.00000 -0.00000 +TI 2 Torsion 3.41210 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 3.3247 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -31.49545 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -31.49545 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -31.4955 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.32091 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.24927 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.3209 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 216.88628 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 475.99774 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 216.8863 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -106.05009 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 45.75437 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -106.0501 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 167.15814 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -44.78635 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02533 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01426 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21636.675763 +Energy at 0.0667 = -21633.727486 +Energy at 0.1333 = -21615.492148 +Energy at 0.2000 = -21572.777453 +Energy at 0.2667 = -21502.067267 +Energy at 0.3333 = -21404.465165 +Energy at 0.4000 = -21284.594759 +Energy at 0.4667 = -21149.680534 +Energy at 0.5333 = -21008.540555 +Energy at 0.6000 = -20870.585735 +Energy at 0.6667 = -20745.078069 +Energy at 0.7333 = -20640.223950 +Energy at 0.8000 = -20562.206391 +Energy at 0.8667 = -20513.939467 +Energy at 0.9333 = -20493.003532 +Energy at 1.0000 = -20489.597473 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 3200 TIME(PS) = 6.400 TEMP(K) = 303.93 PRESS = 0.0 + Etot = -17726.5908 EKtot = 3910.0849 EPtot = -21636.6758 + BOND = 8.3859 ANGLE = 101.8274 DIHED = 6.7247 + 1-4 NB = 6.3378 1-4 EEL = -35.1636 VDWAALS = 3229.2522 + EELEC = -24955.5285 EHBOND = 0.0000 RESTRAINT = 1.4883 + EAMBER (non-restraint) = -21638.1641 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65208.6675 + Density = 0.9972 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4365 SC_EKtot= 0.0000 SC_EPtot = 0.4365 + SC_BOND= 0.0000 SC_ANGLE= 0.4353 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 3200 TIME(PS) = 6.400 TEMP(K) = 303.93 PRESS = 0.0 + Etot = -17726.5908 EKtot = 3910.0849 EPtot = -21636.6758 + BOND = 8.3859 ANGLE = 101.8274 DIHED = 6.7247 + 1-4 NB = 6.3378 1-4 EEL = -35.1636 VDWAALS = 3229.2522 + EELEC = -24955.5285 EHBOND = 0.0000 RESTRAINT = 1.4883 + EAMBER (non-restraint) = -21638.1641 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65208.6675 + Density = 0.9972 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4365 SC_EKtot= 0.0000 SC_EPtot = 0.4365 + SC_BOND= 0.0000 SC_ANGLE= 0.4353 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -8.21705 1.00000 0.00000 -0.00000 +TI 2 vDW -8.64757 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -8.2171 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.38594 1.00000 0.00000 -0.00000 +TI 2 Bond 449.42071 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.3859 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.82739 1.00000 0.00000 -0.00000 +TI 2 Angle 231.54385 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.8274 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.72471 1.00000 0.00000 -0.00000 +TI 2 Torsion 8.35504 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.7247 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -35.16364 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -35.16364 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -35.1636 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.33779 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.26012 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.3378 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 203.81294 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 493.62207 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 203.8129 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -111.11116 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 38.90187 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -111.1112 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 180.96351 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -48.97079 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02537 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0254 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01428 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21570.753317 +Energy at 0.0667 = -21567.832241 +Energy at 0.1333 = -21549.765803 +Energy at 0.2000 = -21507.451277 +Energy at 0.2667 = -21437.418282 +Energy at 0.3333 = -21340.784069 +Energy at 0.4000 = -21222.162933 +Energy at 0.4667 = -21088.752313 +Energy at 0.5333 = -20949.331348 +Energy at 0.6000 = -20813.267243 +Energy at 0.6667 = -20689.774196 +Energy at 0.7333 = -20586.985008 +Energy at 0.8000 = -20510.910664 +Energy at 0.8667 = -20464.136109 +Energy at 0.9333 = -20443.946437 +Energy at 1.0000 = -20440.668638 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 3400 TIME(PS) = 6.800 TEMP(K) = 301.08 PRESS = 0.0 + Etot = -17697.2757 EKtot = 3873.4776 EPtot = -21570.7533 + BOND = 5.3855 ANGLE = 106.3446 DIHED = 7.6015 + 1-4 NB = 5.5390 1-4 EEL = -33.1186 VDWAALS = 2924.8623 + EELEC = -24588.0728 EHBOND = 0.0000 RESTRAINT = 0.7052 + EAMBER (non-restraint) = -21571.4586 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.0805 SC_EKtot= 0.0000 SC_EPtot = 1.0805 + SC_BOND= 0.0000 SC_ANGLE= 1.0792 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 3400 TIME(PS) = 6.800 TEMP(K) = 301.08 PRESS = 0.0 + Etot = -17697.2757 EKtot = 3873.4776 EPtot = -21570.7533 + BOND = 5.3855 ANGLE = 106.3446 DIHED = 7.6015 + 1-4 NB = 5.5390 1-4 EEL = -33.1186 VDWAALS = 2924.8623 + EELEC = -24588.0728 EHBOND = 0.0000 RESTRAINT = 0.7052 + EAMBER (non-restraint) = -21571.4586 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.0805 SC_EKtot= 0.0000 SC_EPtot = 1.0805 + SC_BOND= 0.0000 SC_ANGLE= 1.0792 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -13.04877 1.00000 0.00000 -0.00000 +TI 2 vDW -13.47866 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -13.0488 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.38554 1.00000 0.00000 -0.00000 +TI 2 Bond 527.65272 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.3855 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 106.34458 1.00000 0.00000 -0.00000 +TI 2 Angle 216.25597 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 106.3446 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 7.60148 1.00000 0.00000 -0.00000 +TI 2 Torsion 8.04906 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 7.6015 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.11856 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.11856 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.1186 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.53895 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.47005 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.5390 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 219.29645 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 467.35626 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 219.2964 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -93.18783 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 38.29211 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -93.1878 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 168.34963 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.49142 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02497 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01405 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21620.534968 +Energy at 0.0667 = -21617.649215 +Energy at 0.1333 = -21599.800909 +Energy at 0.2000 = -21557.994948 +Energy at 0.2667 = -21488.796041 +Energy at 0.3333 = -21393.295529 +Energy at 0.4000 = -21276.034527 +Energy at 0.4667 = -21144.103101 +Energy at 0.5333 = -21006.153975 +Energy at 0.6000 = -20871.424703 +Energy at 0.6667 = -20749.011683 +Energy at 0.7333 = -20646.966238 +Energy at 0.8000 = -20571.291125 +Energy at 0.8667 = -20524.661550 +Energy at 0.9333 = -20504.501752 +Energy at 1.0000 = -20501.226605 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 3600 TIME(PS) = 7.200 TEMP(K) = 303.05 PRESS = 0.0 + Etot = -17721.8316 EKtot = 3898.7034 EPtot = -21620.5350 + BOND = 6.8647 ANGLE = 98.7520 DIHED = 6.1578 + 1-4 NB = 7.4488 1-4 EEL = -31.9187 VDWAALS = 3183.4873 + EELEC = -24892.7345 EHBOND = 0.0000 RESTRAINT = 1.4076 + EAMBER (non-restraint) = -21621.9426 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4672 SC_EKtot= 0.0000 SC_EPtot = 0.4672 + SC_BOND= 0.0000 SC_ANGLE= 0.4660 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 3600 TIME(PS) = 7.200 TEMP(K) = 303.05 PRESS = 0.0 + Etot = -17721.8316 EKtot = 3898.7034 EPtot = -21620.5350 + BOND = 6.8647 ANGLE = 98.7520 DIHED = 6.1578 + 1-4 NB = 7.4488 1-4 EEL = -31.9187 VDWAALS = 3183.4873 + EELEC = -24892.7345 EHBOND = 0.0000 RESTRAINT = 1.4076 + EAMBER (non-restraint) = -21621.9426 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4672 SC_EKtot= 0.0000 SC_EPtot = 0.4672 + SC_BOND= 0.0000 SC_ANGLE= 0.4660 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -8.65558 1.00000 0.00000 -0.00000 +TI 2 vDW -9.07319 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -8.6556 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.86467 1.00000 0.00000 -0.00000 +TI 2 Bond 470.73062 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.8647 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 98.75200 1.00000 0.00000 -0.00000 +TI 2 Angle 223.62427 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 98.7520 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.15779 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.26034 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.1578 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -31.91872 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -31.91872 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -31.9187 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 7.44883 1.00000 0.00000 -0.00000 +TI 2 VDW14 7.37722 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 7.4488 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 217.30586 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 490.68307 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 217.3059 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -98.76083 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 36.43083 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -98.7608 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 170.84193 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.44447 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02510 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0251 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01413 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21558.858354 +Energy at 0.0667 = -21555.955291 +Energy at 0.1333 = -21538.000553 +Energy at 0.2000 = -21495.949575 +Energy at 0.2667 = -21426.358403 +Energy at 0.3333 = -21330.343731 +Energy at 0.4000 = -21212.492464 +Energy at 0.4667 = -21079.940243 +Energy at 0.5333 = -20941.355480 +Energy at 0.6000 = -20805.928767 +Energy at 0.6667 = -20682.635698 +Energy at 0.7333 = -20579.396791 +Energy at 0.8000 = -20502.259797 +Energy at 0.8667 = -20454.289042 +Energy at 0.9333 = -20433.394957 +Energy at 1.0000 = -20429.989705 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 3800 TIME(PS) = 7.600 TEMP(K) = 301.74 PRESS = 0.0 + Etot = -17676.9082 EKtot = 3881.9502 EPtot = -21558.8584 + BOND = 8.3346 ANGLE = 99.4578 DIHED = 5.6245 + 1-4 NB = 6.5302 1-4 EEL = -32.9323 VDWAALS = 3115.0040 + EELEC = -24764.4971 EHBOND = 0.0000 RESTRAINT = 3.6199 + EAMBER (non-restraint) = -21562.4782 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.2471 SC_EKtot= 0.0000 SC_EPtot = 0.2471 + SC_BOND= 0.0000 SC_ANGLE= 0.2459 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 3800 TIME(PS) = 7.600 TEMP(K) = 301.74 PRESS = 0.0 + Etot = -17676.9082 EKtot = 3881.9502 EPtot = -21558.8584 + BOND = 8.3346 ANGLE = 99.4578 DIHED = 5.6245 + 1-4 NB = 6.5302 1-4 EEL = -32.9323 VDWAALS = 3115.0040 + EELEC = -24764.4971 EHBOND = 0.0000 RESTRAINT = 3.6199 + EAMBER (non-restraint) = -21562.4782 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.2471 SC_EKtot= 0.0000 SC_EPtot = 0.2471 + SC_BOND= 0.0000 SC_ANGLE= 0.2459 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -3.48039 1.00000 0.00000 -0.00000 +TI 2 vDW -3.86959 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -3.4804 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.33462 1.00000 0.00000 -0.00000 +TI 2 Bond 465.88319 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.3346 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.45781 1.00000 0.00000 -0.00000 +TI 2 Angle 228.20237 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.4578 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.62446 1.00000 0.00000 -0.00000 +TI 2 Torsion 9.75541 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.6245 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.93228 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.93228 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.9323 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.53022 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.45740 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.5302 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 222.12029 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 502.40097 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 222.1203 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -104.28216 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 35.33373 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -104.2822 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 163.82185 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.88642 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02520 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01418 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21500.129621 +Energy at 0.0667 = -21497.210707 +Energy at 0.1333 = -21479.155604 +Energy at 0.2000 = -21436.853349 +Energy at 0.2667 = -21366.792592 +Energy at 0.3333 = -21270.005528 +Energy at 0.4000 = -21150.969147 +Energy at 0.4667 = -21016.683469 +Energy at 0.5333 = -20875.662775 +Energy at 0.6000 = -20736.949299 +Energy at 0.6667 = -20609.451161 +Energy at 0.7333 = -20501.264267 +Energy at 0.8000 = -20419.083057 +Energy at 0.8667 = -20367.110594 +Energy at 0.9333 = -20344.198295 +Energy at 1.0000 = -20340.445676 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 296.50 PRESS = 0.0 + Etot = -17685.6212 EKtot = 3814.5085 EPtot = -21500.1296 + BOND = 7.4160 ANGLE = 97.2063 DIHED = 6.0130 + 1-4 NB = 6.1723 1-4 EEL = -34.0112 VDWAALS = 3111.2082 + EELEC = -24697.4527 EHBOND = 0.0000 RESTRAINT = 3.3186 + EAMBER (non-restraint) = -21503.4482 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4673 SC_EKtot= 0.0000 SC_EPtot = 0.4673 + SC_BOND= 0.0000 SC_ANGLE= 0.4661 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 4000 TIME(PS) = 8.000 TEMP(K) = 296.50 PRESS = 0.0 + Etot = -17685.6212 EKtot = 3814.5085 EPtot = -21500.1296 + BOND = 7.4160 ANGLE = 97.2063 DIHED = 6.0130 + 1-4 NB = 6.1723 1-4 EEL = -34.0112 VDWAALS = 3111.2082 + EELEC = -24697.4527 EHBOND = 0.0000 RESTRAINT = 3.3186 + EAMBER (non-restraint) = -21503.4482 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65677.3141 + Density = 0.9900 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 4 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4673 SC_EKtot= 0.0000 SC_EPtot = 0.4673 + SC_BOND= 0.0000 SC_ANGLE= 0.4661 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -3.56113 1.00000 0.00000 -0.00000 +TI 2 vDW -4.00196 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -3.5611 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 7.41596 1.00000 0.00000 -0.00000 +TI 2 Bond 445.11616 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 7.4160 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 97.20626 1.00000 0.00000 -0.00000 +TI 2 Angle 210.65476 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 97.2063 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.01295 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.48602 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.0130 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.01122 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.01122 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.0112 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.17227 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.10526 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.1723 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 231.81982 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 525.37592 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 231.8198 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -117.40351 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 34.35497 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -117.4035 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 184.33582 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.06375 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02495 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01404 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21527.483254 +Energy at 0.0667 = -21524.568884 +Energy at 0.1333 = -21506.544786 +Energy at 0.2000 = -21464.335393 +Energy at 0.2667 = -21394.496003 +Energy at 0.3333 = -21298.173482 +Energy at 0.4000 = -21180.016627 +Energy at 0.4667 = -21047.256933 +Energy at 0.5333 = -20908.694133 +Energy at 0.6000 = -20773.680290 +Energy at 0.6667 = -20651.349979 +Energy at 0.7333 = -20549.681789 +Energy at 0.8000 = -20474.503450 +Energy at 0.8667 = -20428.285769 +Energy at 0.9333 = -20408.331546 +Energy at 1.0000 = -20405.091429 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 4200 TIME(PS) = 8.400 TEMP(K) = 297.84 PRESS = 0.0 + Etot = -17695.7669 EKtot = 3831.7164 EPtot = -21527.4833 + BOND = 6.1072 ANGLE = 101.7050 DIHED = 7.0768 + 1-4 NB = 5.6410 1-4 EEL = -32.9476 VDWAALS = 3139.3166 + EELEC = -24756.1875 EHBOND = 0.0000 RESTRAINT = 1.8052 + EAMBER (non-restraint) = -21529.2884 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65760.8074 + Density = 0.9888 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8446 SC_EKtot= 0.0000 SC_EPtot = 0.8446 + SC_BOND= 0.0000 SC_ANGLE= 0.8434 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 4200 TIME(PS) = 8.400 TEMP(K) = 297.84 PRESS = 0.0 + Etot = -17695.7669 EKtot = 3831.7164 EPtot = -21527.4833 + BOND = 6.1072 ANGLE = 101.7050 DIHED = 7.0768 + 1-4 NB = 5.6410 1-4 EEL = -32.9476 VDWAALS = 3139.3166 + EELEC = -24756.1875 EHBOND = 0.0000 RESTRAINT = 1.8052 + EAMBER (non-restraint) = -21529.2884 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65760.8074 + Density = 0.9888 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8446 SC_EKtot= 0.0000 SC_EPtot = 0.8446 + SC_BOND= 0.0000 SC_ANGLE= 0.8434 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -8.61069 1.00000 0.00000 -0.00000 +TI 2 vDW -8.97742 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -8.6107 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.10722 1.00000 0.00000 -0.00000 +TI 2 Bond 468.56987 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.1072 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.70501 1.00000 0.00000 -0.00000 +TI 2 Angle 221.35181 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.7050 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 7.07678 1.00000 0.00000 -0.00000 +TI 2 Torsion 7.65254 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 7.0768 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.94758 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.94758 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.9476 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.64102 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.56961 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.6410 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 219.68016 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 510.05374 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 219.6802 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -99.86420 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 42.77718 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -99.8642 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 161.70435 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.94090 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02473 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0247 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01392 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21638.915834 +Energy at 0.0667 = -21635.819380 +Energy at 0.1333 = -21616.668315 +Energy at 0.2000 = -21571.813788 +Energy at 0.2667 = -21497.577916 +Energy at 0.3333 = -21395.145495 +Energy at 0.4000 = -21269.405026 +Energy at 0.4667 = -21127.973228 +Energy at 0.5333 = -20980.120490 +Energy at 0.6000 = -20835.698348 +Energy at 0.6667 = -20704.342024 +Energy at 0.7333 = -20594.530956 +Energy at 0.8000 = -20512.655515 +Energy at 0.8667 = -20461.835251 +Energy at 0.9333 = -20439.725264 +Energy at 1.0000 = -20436.123258 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 4400 TIME(PS) = 8.800 TEMP(K) = 298.26 PRESS = 0.0 + Etot = -17801.8280 EKtot = 3837.0878 EPtot = -21638.9158 + BOND = 11.0994 ANGLE = 101.1127 DIHED = 3.9811 + 1-4 NB = 6.3130 1-4 EEL = -34.3778 VDWAALS = 3050.8056 + EELEC = -24779.9346 EHBOND = 0.0000 RESTRAINT = 2.0848 + EAMBER (non-restraint) = -21641.0006 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65836.5316 + Density = 0.9877 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3795 SC_EKtot= 0.0000 SC_EPtot = 0.3795 + SC_BOND= 0.0000 SC_ANGLE= 0.3783 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 4400 TIME(PS) = 8.800 TEMP(K) = 298.26 PRESS = 0.0 + Etot = -17801.8280 EKtot = 3837.0878 EPtot = -21638.9158 + BOND = 11.0994 ANGLE = 101.1127 DIHED = 3.9811 + 1-4 NB = 6.3130 1-4 EEL = -34.3778 VDWAALS = 3050.8056 + EELEC = -24779.9346 EHBOND = 0.0000 RESTRAINT = 2.0848 + EAMBER (non-restraint) = -21641.0006 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65836.5316 + Density = 0.9877 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3795 SC_EKtot= 0.0000 SC_EPtot = 0.3795 + SC_BOND= 0.0000 SC_ANGLE= 0.3783 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -11.84525 1.00000 0.00000 -0.00000 +TI 2 vDW -12.24295 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -11.8453 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 11.09940 1.00000 0.00000 -0.00000 +TI 2 Bond 553.05749 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 11.0994 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.11268 1.00000 0.00000 -0.00000 +TI 2 Angle 220.01920 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.1127 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 3.98113 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.86259 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 3.9811 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.37783 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.37783 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.3778 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.31299 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.23619 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.3130 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 222.85080 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 496.64600 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 222.8508 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -99.82913 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 38.11868 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -99.8291 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 173.49665 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -48.42504 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02478 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01395 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21556.321345 +Energy at 0.0667 = -21553.545696 +Energy at 0.1333 = -21536.378954 +Energy at 0.2000 = -21496.173310 +Energy at 0.2667 = -21429.635669 +Energy at 0.3333 = -21337.834303 +Energy at 0.4000 = -21225.158834 +Energy at 0.4667 = -21098.444029 +Energy at 0.5333 = -20966.006036 +Energy at 0.6000 = -20836.685238 +Energy at 0.6667 = -20719.142929 +Energy at 0.7333 = -20621.025847 +Energy at 0.8000 = -20548.084956 +Energy at 0.8667 = -20503.006516 +Energy at 0.9333 = -20483.472568 +Energy at 1.0000 = -20480.296053 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 4600 TIME(PS) = 9.200 TEMP(K) = 295.64 PRESS = 0.0 + Etot = -17752.9180 EKtot = 3803.4034 EPtot = -21556.3213 + BOND = 12.4781 ANGLE = 101.7115 DIHED = 8.0907 + 1-4 NB = 5.1985 1-4 EEL = -33.1463 VDWAALS = 3201.7451 + EELEC = -24855.0958 EHBOND = 0.0000 RESTRAINT = 2.6968 + EAMBER (non-restraint) = -21559.0182 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65481.5348 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.5294 SC_EKtot= 0.0000 SC_EPtot = 1.5294 + SC_BOND= 0.0000 SC_ANGLE= 1.5282 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 4600 TIME(PS) = 9.200 TEMP(K) = 295.64 PRESS = 0.0 + Etot = -17752.9180 EKtot = 3803.4034 EPtot = -21556.3213 + BOND = 12.4781 ANGLE = 101.7115 DIHED = 8.0907 + 1-4 NB = 5.1985 1-4 EEL = -33.1463 VDWAALS = 3201.7451 + EELEC = -24855.0958 EHBOND = 0.0000 RESTRAINT = 2.6968 + EAMBER (non-restraint) = -21559.0182 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65481.5348 + Density = 0.9930 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.5294 SC_EKtot= 0.0000 SC_EPtot = 1.5294 + SC_BOND= 0.0000 SC_ANGLE= 1.5282 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -9.12320 1.00000 0.00000 -0.00000 +TI 2 vDW -9.50847 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -9.1232 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 12.47805 1.00000 0.00000 -0.00000 +TI 2 Bond 429.49830 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 12.4781 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.71155 1.00000 0.00000 -0.00000 +TI 2 Angle 233.26619 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.7115 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 8.09068 1.00000 0.00000 -0.00000 +TI 2 Torsion 7.65245 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 8.0907 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.14630 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.14630 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.1463 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.19851 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.12864 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.1985 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 220.67300 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 487.78726 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 220.6730 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -98.89345 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 49.83397 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -98.8935 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 161.98967 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.34978 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02504 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01410 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21637.067409 +Energy at 0.0667 = -21633.973003 +Energy at 0.1333 = -21614.835372 +Energy at 0.2000 = -21570.017721 +Energy at 0.2667 = -21495.861165 +Energy at 0.3333 = -21393.582037 +Energy at 0.4000 = -21268.117929 +Energy at 0.4667 = -21127.158220 +Energy at 0.5333 = -20980.077793 +Energy at 0.6000 = -20836.869780 +Energy at 0.6667 = -20707.323464 +Energy at 0.7333 = -20599.974668 +Energy at 0.8000 = -20520.940697 +Energy at 0.8667 = -20472.587000 +Energy at 0.9333 = -20451.785727 +Energy at 1.0000 = -20448.413082 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 4800 TIME(PS) = 9.600 TEMP(K) = 299.85 PRESS = 0.0 + Etot = -17779.5258 EKtot = 3857.5416 EPtot = -21637.0674 + BOND = 5.9423 ANGLE = 93.9982 DIHED = 4.2117 + 1-4 NB = 6.3426 1-4 EEL = -32.2433 VDWAALS = 3102.7309 + EELEC = -24822.6406 EHBOND = 0.0000 RESTRAINT = 4.5908 + EAMBER (non-restraint) = -21641.6582 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65761.8146 + Density = 0.9888 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3642 SC_EKtot= 0.0000 SC_EPtot = 0.3642 + SC_BOND= 0.0000 SC_ANGLE= 0.3630 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 4800 TIME(PS) = 9.600 TEMP(K) = 299.85 PRESS = 0.0 + Etot = -17779.5258 EKtot = 3857.5416 EPtot = -21637.0674 + BOND = 5.9423 ANGLE = 93.9982 DIHED = 4.2117 + 1-4 NB = 6.3426 1-4 EEL = -32.2433 VDWAALS = 3102.7309 + EELEC = -24822.6406 EHBOND = 0.0000 RESTRAINT = 4.5908 + EAMBER (non-restraint) = -21641.6582 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65761.8146 + Density = 0.9888 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3642 SC_EKtot= 0.0000 SC_EPtot = 0.3642 + SC_BOND= 0.0000 SC_ANGLE= 0.3630 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW 1.52363 1.00000 0.00000 -0.00000 +TI 2 vDW 1.10934 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= 1.5236 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.94226 1.00000 0.00000 -0.00000 +TI 2 Bond 504.99719 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.9423 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 93.99821 1.00000 0.00000 -0.00000 +TI 2 Angle 222.71132 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 93.9982 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.21172 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.62046 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.2117 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.24333 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.24333 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.2433 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.34262 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.26766 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.3426 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 221.42990 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 512.75879 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 221.4299 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -110.37978 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 50.94065 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -110.3798 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 164.91469 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.92449 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02494 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0249 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01404 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21617.126081 +Energy at 0.0667 = -21614.041341 +Energy at 0.1333 = -21594.962113 +Energy at 0.2000 = -21550.271472 +Energy at 0.2667 = -21476.291715 +Energy at 0.3333 = -21374.175213 +Energy at 0.4000 = -21248.745077 +Energy at 0.4667 = -21107.519993 +Energy at 0.5333 = -20959.645976 +Energy at 0.6000 = -20814.845615 +Energy at 0.6667 = -20682.674618 +Energy at 0.7333 = -20571.673789 +Energy at 0.8000 = -20488.505873 +Energy at 0.8667 = -20436.682196 +Energy at 0.9333 = -20414.088353 +Energy at 1.0000 = -20410.405029 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 295.71 PRESS = 0.0 + Etot = -17812.7581 EKtot = 3804.3679 EPtot = -21617.1261 + BOND = 5.8363 ANGLE = 101.4794 DIHED = 5.5052 + 1-4 NB = 8.2027 1-4 EEL = -34.0607 VDWAALS = 3122.2737 + EELEC = -24830.2981 EHBOND = 0.0000 RESTRAINT = 3.9354 + EAMBER (non-restraint) = -21621.0615 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65706.6962 + Density = 0.9896 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7065 SC_EKtot= 0.0000 SC_EPtot = 0.7065 + SC_BOND= 0.0000 SC_ANGLE= 0.7053 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 5000 TIME(PS) = 10.000 TEMP(K) = 295.71 PRESS = 0.0 + Etot = -17812.7581 EKtot = 3804.3679 EPtot = -21617.1261 + BOND = 5.8363 ANGLE = 101.4794 DIHED = 5.5052 + 1-4 NB = 8.2027 1-4 EEL = -34.0607 VDWAALS = 3122.2737 + EELEC = -24830.2981 EHBOND = 0.0000 RESTRAINT = 3.9354 + EAMBER (non-restraint) = -21621.0615 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65706.6962 + Density = 0.9896 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 5 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7065 SC_EKtot= 0.0000 SC_EPtot = 0.7065 + SC_BOND= 0.0000 SC_ANGLE= 0.7053 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -6.05175 1.00000 0.00000 -0.00000 +TI 2 vDW -6.46570 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -6.0518 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.83633 1.00000 0.00000 -0.00000 +TI 2 Bond 525.29585 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.8363 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 101.47936 1.00000 0.00000 -0.00000 +TI 2 Angle 215.42380 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 101.4794 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.50520 1.00000 0.00000 -0.00000 +TI 2 Torsion 8.18901 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.5052 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.06070 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.06070 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.0607 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 8.20268 1.00000 0.00000 -0.00000 +TI 2 VDW14 8.13455 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 8.2027 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 206.93864 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 499.26920 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 206.9386 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -104.79876 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 38.70826 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -104.7988 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 170.83375 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.57490 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02496 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01405 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21637.864251 +Energy at 0.0667 = -21635.196767 +Energy at 0.1333 = -21618.699842 +Energy at 0.2000 = -21580.068859 +Energy at 0.2667 = -21516.156804 +Energy at 0.3333 = -21428.023640 +Energy at 0.4000 = -21319.938062 +Energy at 0.4667 = -21198.534087 +Energy at 0.5333 = -21071.880033 +Energy at 0.6000 = -20948.545762 +Energy at 0.6667 = -20836.892749 +Energy at 0.7333 = -20744.204532 +Energy at 0.8000 = -20675.762294 +Energy at 0.8667 = -20633.744703 +Energy at 0.9333 = -20615.621888 +Energy at 1.0000 = -20612.680335 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 5200 TIME(PS) = 10.400 TEMP(K) = 297.35 PRESS = 0.0 + Etot = -17812.4124 EKtot = 3825.4518 EPtot = -21637.8643 + BOND = 11.6817 ANGLE = 100.2644 DIHED = 6.4818 + 1-4 NB = 6.8818 1-4 EEL = -34.5082 VDWAALS = 3066.7091 + EELEC = -24799.8659 EHBOND = 0.0000 RESTRAINT = 4.4910 + EAMBER (non-restraint) = -21642.3553 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65706.6962 + Density = 0.9896 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8195 SC_EKtot= 0.0000 SC_EPtot = 0.8195 + SC_BOND= 0.0000 SC_ANGLE= 0.8183 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 5200 TIME(PS) = 10.400 TEMP(K) = 297.35 PRESS = 0.0 + Etot = -17812.4124 EKtot = 3825.4518 EPtot = -21637.8643 + BOND = 11.6817 ANGLE = 100.2644 DIHED = 6.4818 + 1-4 NB = 6.8818 1-4 EEL = -34.5082 VDWAALS = 3066.7091 + EELEC = -24799.8659 EHBOND = 0.0000 RESTRAINT = 4.4910 + EAMBER (non-restraint) = -21642.3553 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65706.6962 + Density = 0.9896 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8195 SC_EKtot= 0.0000 SC_EPtot = 0.8195 + SC_BOND= 0.0000 SC_ANGLE= 0.8183 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -7.09619 1.00000 0.00000 -0.00000 +TI 2 vDW -7.45434 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -7.0962 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 11.68173 1.00000 0.00000 -0.00000 +TI 2 Bond 408.70826 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 11.6817 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.26439 1.00000 0.00000 -0.00000 +TI 2 Angle 232.26009 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.2644 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.48183 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.25556 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.4818 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.50822 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.50822 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.5082 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.88177 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.81397 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.8818 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 213.02293 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 475.42969 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 213.0229 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -86.32472 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 53.08389 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -86.3247 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 157.29208 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.74166 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02481 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01397 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21580.227155 +Energy at 0.0667 = -21577.359142 +Energy at 0.1333 = -21559.619491 +Energy at 0.2000 = -21518.060486 +Energy at 0.2667 = -21449.244353 +Energy at 0.3333 = -21354.207822 +Energy at 0.4000 = -21237.381924 +Energy at 0.4667 = -21105.682391 +Energy at 0.5333 = -20967.509559 +Energy at 0.6000 = -20831.760837 +Energy at 0.6667 = -20707.144908 +Energy at 0.7333 = -20601.472959 +Energy at 0.8000 = -20521.103004 +Energy at 0.8667 = -20470.074314 +Energy at 0.9333 = -20447.469858 +Energy at 1.0000 = -20443.758425 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 5400 TIME(PS) = 10.800 TEMP(K) = 291.87 PRESS = 0.0 + Etot = -17825.2609 EKtot = 3754.9662 EPtot = -21580.2272 + BOND = 10.6212 ANGLE = 99.0612 DIHED = 4.8888 + 1-4 NB = 5.2349 1-4 EEL = -33.0939 VDWAALS = 3045.1244 + EELEC = -24713.9886 EHBOND = 0.0000 RESTRAINT = 1.9248 + EAMBER (non-restraint) = -21582.1519 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65706.6962 + Density = 0.9896 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3376 SC_EKtot= 0.0000 SC_EPtot = 0.3376 + SC_BOND= 0.0000 SC_ANGLE= 0.3364 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 5400 TIME(PS) = 10.800 TEMP(K) = 291.87 PRESS = 0.0 + Etot = -17825.2609 EKtot = 3754.9662 EPtot = -21580.2272 + BOND = 10.6212 ANGLE = 99.0612 DIHED = 4.8888 + 1-4 NB = 5.2349 1-4 EEL = -33.0939 VDWAALS = 3045.1244 + EELEC = -24713.9886 EHBOND = 0.0000 RESTRAINT = 1.9248 + EAMBER (non-restraint) = -21582.1519 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65706.6962 + Density = 0.9896 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3376 SC_EKtot= 0.0000 SC_EPtot = 0.3376 + SC_BOND= 0.0000 SC_ANGLE= 0.3364 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -1.44071 1.00000 0.00000 -0.00000 +TI 2 vDW -1.88770 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -1.4407 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 10.62122 1.00000 0.00000 -0.00000 +TI 2 Bond 444.71719 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 10.6212 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.06120 1.00000 0.00000 -0.00000 +TI 2 Angle 227.45654 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.0612 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.88882 1.00000 0.00000 -0.00000 +TI 2 Torsion 7.51223 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.8888 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.09387 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.09387 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.0939 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.23486 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.16242 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.2349 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 224.22340 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 496.11530 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 224.2234 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -110.02766 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 36.95078 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -110.0277 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 176.91694 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.70477 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02478 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01394 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21585.969771 +Energy at 0.0667 = -21583.188720 +Energy at 0.1333 = -21565.988203 +Energy at 0.2000 = -21525.701045 +Energy at 0.2667 = -21459.021211 +Energy at 0.3333 = -21367.009523 +Energy at 0.4000 = -21254.056722 +Energy at 0.4667 = -21127.015015 +Energy at 0.5333 = -20994.244585 +Energy at 0.6000 = -20864.663252 +Energy at 0.6667 = -20747.032435 +Energy at 0.7333 = -20649.071720 +Energy at 0.8000 = -20576.494282 +Energy at 0.8667 = -20531.805262 +Energy at 0.9333 = -20512.492244 +Energy at 1.0000 = -20509.355105 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 5600 TIME(PS) = 11.200 TEMP(K) = 297.94 PRESS = 0.0 + Etot = -17752.9066 EKtot = 3833.0631 EPtot = -21585.9698 + BOND = 5.3843 ANGLE = 98.3557 DIHED = 5.1483 + 1-4 NB = 5.9090 1-4 EEL = -33.4668 VDWAALS = 3179.3053 + EELEC = -24848.1327 EHBOND = 0.0000 RESTRAINT = 1.5271 + EAMBER (non-restraint) = -21587.4969 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65720.0265 + Density = 0.9894 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3557 SC_EKtot= 0.0000 SC_EPtot = 0.3557 + SC_BOND= 0.0000 SC_ANGLE= 0.3545 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 5600 TIME(PS) = 11.200 TEMP(K) = 297.94 PRESS = 0.0 + Etot = -17752.9066 EKtot = 3833.0631 EPtot = -21585.9698 + BOND = 5.3843 ANGLE = 98.3557 DIHED = 5.1483 + 1-4 NB = 5.9090 1-4 EEL = -33.4668 VDWAALS = 3179.3053 + EELEC = -24848.1327 EHBOND = 0.0000 RESTRAINT = 1.5271 + EAMBER (non-restraint) = -21587.4969 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65720.0265 + Density = 0.9894 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3557 SC_EKtot= 0.0000 SC_EPtot = 0.3557 + SC_BOND= 0.0000 SC_ANGLE= 0.3545 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -17.62156 1.00000 0.00000 -0.00000 +TI 2 vDW -17.99108 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -17.6216 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.38432 1.00000 0.00000 -0.00000 +TI 2 Bond 442.52325 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.3843 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 98.35574 1.00000 0.00000 -0.00000 +TI 2 Angle 229.75406 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 98.3557 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.14830 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.96256 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.1483 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.46679 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.46679 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.4668 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.90896 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.84220 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.9090 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 217.68610 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 470.59909 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 217.6861 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -88.29676 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 49.45128 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -88.2968 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 168.90147 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.29787 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02484 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01398 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21464.954564 +Energy at 0.0667 = -21461.903442 +Energy at 0.1333 = -21443.031104 +Energy at 0.2000 = -21398.817891 +Energy at 0.2667 = -21325.604982 +Energy at 0.3333 = -21224.493760 +Energy at 0.4000 = -21100.199694 +Energy at 0.4667 = -20960.090929 +Energy at 0.5333 = -20813.135405 +Energy at 0.6000 = -20668.867581 +Energy at 0.6667 = -20536.677333 +Energy at 0.7333 = -20425.041915 +Energy at 0.8000 = -20340.793935 +Energy at 0.8667 = -20287.900737 +Energy at 0.9333 = -20264.713213 +Energy at 1.0000 = -20260.924552 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 5800 TIME(PS) = 11.600 TEMP(K) = 291.80 PRESS = 0.0 + Etot = -17710.9387 EKtot = 3754.0159 EPtot = -21464.9546 + BOND = 5.1522 ANGLE = 99.1763 DIHED = 6.8836 + 1-4 NB = 7.8681 1-4 EEL = -33.2854 VDWAALS = 2994.9207 + EELEC = -24549.8770 EHBOND = 0.0000 RESTRAINT = 4.2069 + EAMBER (non-restraint) = -21469.1615 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65720.0265 + Density = 0.9894 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6549 SC_EKtot= 0.0000 SC_EPtot = 0.6549 + SC_BOND= 0.0000 SC_ANGLE= 0.6537 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 5800 TIME(PS) = 11.600 TEMP(K) = 291.80 PRESS = 0.0 + Etot = -17710.9387 EKtot = 3754.0159 EPtot = -21464.9546 + BOND = 5.1522 ANGLE = 99.1763 DIHED = 6.8836 + 1-4 NB = 7.8681 1-4 EEL = -33.2854 VDWAALS = 2994.9207 + EELEC = -24549.8770 EHBOND = 0.0000 RESTRAINT = 4.2069 + EAMBER (non-restraint) = -21469.1615 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65720.0265 + Density = 0.9894 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6549 SC_EKtot= 0.0000 SC_EPtot = 0.6549 + SC_BOND= 0.0000 SC_ANGLE= 0.6537 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -3.04450 1.00000 0.00000 -0.00000 +TI 2 vDW -3.51089 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -3.0445 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.15224 1.00000 0.00000 -0.00000 +TI 2 Bond 482.58375 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.1522 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.17630 1.00000 0.00000 -0.00000 +TI 2 Angle 235.59340 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.1763 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.88358 1.00000 0.00000 -0.00000 +TI 2 Torsion 8.92411 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.8836 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.28543 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.28543 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.2854 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 7.86809 1.00000 0.00000 -0.00000 +TI 2 VDW14 7.80510 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 7.8681 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 212.33005 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 499.17523 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 212.3300 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -113.13409 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 32.36572 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -113.1341 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 180.30164 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.88005 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02512 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0251 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01414 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21469.648645 +Energy at 0.0667 = -21466.810660 +Energy at 0.1333 = -21449.257737 +Energy at 0.2000 = -21408.143198 +Energy at 0.2667 = -21340.086866 +Energy at 0.3333 = -21246.157150 +Energy at 0.4000 = -21130.808066 +Energy at 0.4667 = -21000.985605 +Energy at 0.5333 = -20865.144845 +Energy at 0.6000 = -20732.272793 +Energy at 0.6667 = -20611.175830 +Energy at 0.7333 = -20509.659001 +Energy at 0.8000 = -20433.719761 +Energy at 0.8667 = -20386.444341 +Energy at 0.9333 = -20365.838623 +Energy at 1.0000 = -20362.479434 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 289.28 PRESS = 0.0 + Etot = -17748.0736 EKtot = 3721.5750 EPtot = -21469.6486 + BOND = 9.5151 ANGLE = 105.3020 DIHED = 4.9798 + 1-4 NB = 5.3945 1-4 EEL = -35.0008 VDWAALS = 2891.3161 + EELEC = -24453.2710 EHBOND = 0.0000 RESTRAINT = 2.1156 + EAMBER (non-restraint) = -21471.7642 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65974.6912 + Density = 0.9856 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3370 SC_EKtot= 0.0000 SC_EPtot = 0.3370 + SC_BOND= 0.0000 SC_ANGLE= 0.3357 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 6000 TIME(PS) = 12.000 TEMP(K) = 289.28 PRESS = 0.0 + Etot = -17748.0736 EKtot = 3721.5750 EPtot = -21469.6486 + BOND = 9.5151 ANGLE = 105.3020 DIHED = 4.9798 + 1-4 NB = 5.3945 1-4 EEL = -35.0008 VDWAALS = 2891.3161 + EELEC = -24453.2710 EHBOND = 0.0000 RESTRAINT = 2.1156 + EAMBER (non-restraint) = -21471.7642 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65974.6912 + Density = 0.9856 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 6 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3370 SC_EKtot= 0.0000 SC_EPtot = 0.3370 + SC_BOND= 0.0000 SC_ANGLE= 0.3357 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -12.38792 1.00000 0.00000 -0.00000 +TI 2 vDW -12.79484 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -12.3879 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 9.51514 1.00000 0.00000 -0.00000 +TI 2 Bond 426.09293 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 9.5151 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 105.30196 1.00000 0.00000 -0.00000 +TI 2 Angle 228.44701 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 105.3020 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.97977 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.91716 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.9798 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -35.00081 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -35.00081 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -35.0008 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.39454 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.31896 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.3945 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 221.41042 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 505.31647 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 221.4104 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -105.26809 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 48.21890 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -105.2681 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 175.12798 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -49.23779 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02486 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0249 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01399 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21514.318935 +Energy at 0.0667 = -21511.414791 +Energy at 0.1333 = -21493.453877 +Energy at 0.2000 = -21451.392163 +Energy at 0.2667 = -21381.796944 +Energy at 0.3333 = -21285.813869 +Energy at 0.4000 = -21168.087369 +Energy at 0.4667 = -21035.855021 +Energy at 0.5333 = -20897.949158 +Energy at 0.6000 = -20763.790166 +Energy at 0.6667 = -20642.594711 +Energy at 0.7333 = -20542.354674 +Energy at 0.8000 = -20468.715711 +Energy at 0.8667 = -20423.753151 +Energy at 0.9333 = -20404.436207 +Energy at 1.0000 = -20401.305809 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 6200 TIME(PS) = 12.400 TEMP(K) = 294.74 PRESS = 0.0 + Etot = -17722.4268 EKtot = 3791.8921 EPtot = -21514.3189 + BOND = 8.6887 ANGLE = 97.5664 DIHED = 8.4280 + 1-4 NB = 4.7401 1-4 EEL = -35.6504 VDWAALS = 2976.6129 + EELEC = -24580.0691 EHBOND = 0.0000 RESTRAINT = 5.3645 + EAMBER (non-restraint) = -21519.6835 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 66007.4531 + Density = 0.9851 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.2141 SC_EKtot= 0.0000 SC_EPtot = 1.2141 + SC_BOND= 0.0000 SC_ANGLE= 1.2128 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 6200 TIME(PS) = 12.400 TEMP(K) = 294.74 PRESS = 0.0 + Etot = -17722.4268 EKtot = 3791.8921 EPtot = -21514.3189 + BOND = 8.6887 ANGLE = 97.5664 DIHED = 8.4280 + 1-4 NB = 4.7401 1-4 EEL = -35.6504 VDWAALS = 2976.6129 + EELEC = -24580.0691 EHBOND = 0.0000 RESTRAINT = 5.3645 + EAMBER (non-restraint) = -21519.6835 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 66007.4531 + Density = 0.9851 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.2141 SC_EKtot= 0.0000 SC_EPtot = 1.2141 + SC_BOND= 0.0000 SC_ANGLE= 1.2128 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -8.03884 1.00000 0.00000 -0.00000 +TI 2 vDW -8.40478 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -8.0388 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.68871 1.00000 0.00000 -0.00000 +TI 2 Bond 445.16114 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.6887 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 97.56638 1.00000 0.00000 -0.00000 +TI 2 Angle 226.79805 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 97.5664 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 8.42802 1.00000 0.00000 -0.00000 +TI 2 Torsion 9.47864 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 8.4280 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -35.65045 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -35.65045 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -35.6504 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 4.74008 1.00000 0.00000 -0.00000 +TI 2 VDW14 4.66883 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 4.7401 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 226.73819 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 533.45801 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 226.7382 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -83.79551 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 48.37160 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -83.7955 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 171.08759 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -49.08970 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02479 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01395 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21487.651327 +Energy at 0.0667 = -21484.585378 +Energy at 0.1333 = -21465.622664 +Energy at 0.2000 = -21421.207062 +Energy at 0.2667 = -21347.690313 +Energy at 0.3333 = -21246.233432 +Energy at 0.4000 = -21121.659673 +Energy at 0.4667 = -20981.492006 +Energy at 0.5333 = -20834.898043 +Energy at 0.6000 = -20691.646637 +Energy at 0.6667 = -20561.346592 +Energy at 0.7333 = -20452.526030 +Energy at 0.8000 = -20371.626068 +Energy at 0.8667 = -20321.650508 +Energy at 0.9333 = -20300.005683 +Energy at 1.0000 = -20296.486796 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 6400 TIME(PS) = 12.800 TEMP(K) = 295.29 PRESS = 0.0 + Etot = -17688.6830 EKtot = 3798.9683 EPtot = -21487.6513 + BOND = 9.4489 ANGLE = 94.7442 DIHED = 4.3413 + 1-4 NB = 5.2826 1-4 EEL = -32.4900 VDWAALS = 2972.6488 + EELEC = -24544.4500 EHBOND = 0.0000 RESTRAINT = 2.8229 + EAMBER (non-restraint) = -21490.4742 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65759.7059 + Density = 0.9888 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4760 SC_EKtot= 0.0000 SC_EPtot = 0.4760 + SC_BOND= 0.0000 SC_ANGLE= 0.4748 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 6400 TIME(PS) = 12.800 TEMP(K) = 295.29 PRESS = 0.0 + Etot = -17688.6830 EKtot = 3798.9683 EPtot = -21487.6513 + BOND = 9.4489 ANGLE = 94.7442 DIHED = 4.3413 + 1-4 NB = 5.2826 1-4 EEL = -32.4900 VDWAALS = 2972.6488 + EELEC = -24544.4500 EHBOND = 0.0000 RESTRAINT = 2.8229 + EAMBER (non-restraint) = -21490.4742 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65759.7059 + Density = 0.9888 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4760 SC_EKtot= 0.0000 SC_EPtot = 0.4760 + SC_BOND= 0.0000 SC_ANGLE= 0.4748 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -3.18125 1.00000 0.00000 -0.00000 +TI 2 vDW -3.62099 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -3.1813 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 9.44889 1.00000 0.00000 -0.00000 +TI 2 Bond 512.48874 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 9.4489 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 94.74415 1.00000 0.00000 -0.00000 +TI 2 Angle 213.01956 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 94.7442 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.34134 1.00000 0.00000 -0.00000 +TI 2 Torsion 6.30075 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.3413 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.48998 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.48998 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.4900 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.28260 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.21981 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.2826 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 219.67870 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 509.92960 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 219.6787 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -112.57303 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 37.75933 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -112.5730 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 168.99940 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -44.67490 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02494 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0249 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01404 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21546.212176 +Energy at 0.0667 = -21543.440851 +Energy at 0.1333 = -21526.300557 +Energy at 0.2000 = -21486.154882 +Energy at 0.2667 = -21419.710444 +Energy at 0.3333 = -21328.025705 +Energy at 0.4000 = -21215.476437 +Energy at 0.4667 = -21088.888524 +Energy at 0.5333 = -20956.586315 +Energy at 0.6000 = -20827.446128 +Energy at 0.6667 = -20710.188962 +Energy at 0.7333 = -20612.505942 +Energy at 0.8000 = -20540.103342 +Energy at 0.8667 = -20495.502774 +Energy at 0.9333 = -20476.221952 +Energy at 1.0000 = -20473.089630 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 6600 TIME(PS) = 13.200 TEMP(K) = 294.50 PRESS = 0.0 + Etot = -17757.4306 EKtot = 3788.7816 EPtot = -21546.2122 + BOND = 8.5541 ANGLE = 100.8323 DIHED = 4.2854 + 1-4 NB = 5.8872 1-4 EEL = -33.7315 VDWAALS = 3035.9247 + EELEC = -24674.5275 EHBOND = 0.0000 RESTRAINT = 6.5632 + EAMBER (non-restraint) = -21552.7753 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 66057.7287 + Density = 0.9843 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.0140 SC_EKtot= 0.0000 SC_EPtot = 1.0140 + SC_BOND= 0.0000 SC_ANGLE= 1.0128 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 6600 TIME(PS) = 13.200 TEMP(K) = 294.50 PRESS = 0.0 + Etot = -17757.4306 EKtot = 3788.7816 EPtot = -21546.2122 + BOND = 8.5541 ANGLE = 100.8323 DIHED = 4.2854 + 1-4 NB = 5.8872 1-4 EEL = -33.7315 VDWAALS = 3035.9247 + EELEC = -24674.5275 EHBOND = 0.0000 RESTRAINT = 6.5632 + EAMBER (non-restraint) = -21552.7753 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 66057.7287 + Density = 0.9843 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.0140 SC_EKtot= 0.0000 SC_EPtot = 1.0140 + SC_BOND= 0.0000 SC_ANGLE= 1.0128 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -6.06707 1.00000 0.00000 -0.00000 +TI 2 vDW -6.45789 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -6.0671 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.55406 1.00000 0.00000 -0.00000 +TI 2 Bond 414.83692 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.5541 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.83230 1.00000 0.00000 -0.00000 +TI 2 Angle 215.72604 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.8323 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.28539 1.00000 0.00000 -0.00000 +TI 2 Torsion 3.90498 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.2854 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.73147 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.73147 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.7315 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.88722 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.81361 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.8872 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 211.27739 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 504.68399 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 211.2774 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -104.74089 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 37.67636 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -104.7409 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 168.25840 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.86961 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02483 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01397 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21483.124631 +Energy at 0.0667 = -21479.976696 +Energy at 0.1333 = -21460.507423 +Energy at 0.2000 = -21414.908901 +Energy at 0.2667 = -21339.445622 +Energy at 0.3333 = -21235.327204 +Energy at 0.4000 = -21107.527162 +Energy at 0.4667 = -20963.785234 +Energy at 0.5333 = -20813.506199 +Energy at 0.6000 = -20666.660647 +Energy at 0.6667 = -20532.974691 +Energy at 0.7333 = -20421.004574 +Energy at 0.8000 = -20337.262869 +Energy at 0.8667 = -20285.087854 +Energy at 0.9333 = -20262.318364 +Energy at 1.0000 = -20258.603933 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 6800 TIME(PS) = 13.600 TEMP(K) = 298.50 PRESS = 0.0 + Etot = -17642.8617 EKtot = 3840.2629 EPtot = -21483.1246 + BOND = 12.8362 ANGLE = 103.3853 DIHED = 8.1838 + 1-4 NB = 5.6884 1-4 EEL = -32.6110 VDWAALS = 3253.1130 + EELEC = -24839.7345 EHBOND = 0.0000 RESTRAINT = 6.0141 + EAMBER (non-restraint) = -21489.1387 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65653.2057 + Density = 0.9904 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3060 SC_EKtot= 0.0000 SC_EPtot = 0.3060 + SC_BOND= 0.0000 SC_ANGLE= 0.3048 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 6800 TIME(PS) = 13.600 TEMP(K) = 298.50 PRESS = 0.0 + Etot = -17642.8617 EKtot = 3840.2629 EPtot = -21483.1246 + BOND = 12.8362 ANGLE = 103.3853 DIHED = 8.1838 + 1-4 NB = 5.6884 1-4 EEL = -32.6110 VDWAALS = 3253.1130 + EELEC = -24839.7345 EHBOND = 0.0000 RESTRAINT = 6.0141 + EAMBER (non-restraint) = -21489.1387 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65653.2057 + Density = 0.9904 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.3060 SC_EKtot= 0.0000 SC_EPtot = 0.3060 + SC_BOND= 0.0000 SC_ANGLE= 0.3048 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -4.43742 1.00000 0.00000 -0.00000 +TI 2 vDW -4.87633 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -4.4374 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 12.83618 1.00000 0.00000 -0.00000 +TI 2 Bond 503.45376 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 12.8362 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 103.38534 1.00000 0.00000 -0.00000 +TI 2 Angle 247.37670 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 103.3853 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 8.18384 1.00000 0.00000 -0.00000 +TI 2 Torsion 11.85398 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 8.1838 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.61098 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.61098 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.6110 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.68841 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.61822 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.6884 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 220.02791 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 528.95770 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 220.0279 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -112.17262 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 37.64669 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -112.1726 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 168.14144 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.32799 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02498 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01406 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21605.128112 +Energy at 0.0667 = -21602.209389 +Energy at 0.1333 = -21584.157461 +Energy at 0.2000 = -21541.876583 +Energy at 0.2667 = -21471.897641 +Energy at 0.3333 = -21375.331907 +Energy at 0.4000 = -21256.775693 +Energy at 0.4667 = -21123.385666 +Energy at 0.5333 = -20983.858633 +Energy at 0.6000 = -20847.415826 +Energy at 0.6667 = -20723.066023 +Energy at 0.7333 = -20618.778690 +Energy at 0.8000 = -20540.695795 +Energy at 0.8667 = -20492.028384 +Energy at 0.9333 = -20470.795475 +Energy at 1.0000 = -20467.332582 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 302.37 PRESS = 0.0 + Etot = -17715.1160 EKtot = 3890.0121 EPtot = -21605.1281 + BOND = 6.6896 ANGLE = 100.6053 DIHED = 4.6055 + 1-4 NB = 6.4868 1-4 EEL = -32.6310 VDWAALS = 3120.5532 + EELEC = -24812.9365 EHBOND = 0.0000 RESTRAINT = 1.4990 + EAMBER (non-restraint) = -21606.6271 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65653.2057 + Density = 0.9904 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8423 SC_EKtot= 0.0000 SC_EPtot = 0.8423 + SC_BOND= 0.0000 SC_ANGLE= 0.8410 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 302.37 PRESS = 0.0 + Etot = -17715.1160 EKtot = 3890.0121 EPtot = -21605.1281 + BOND = 6.6896 ANGLE = 100.6053 DIHED = 4.6055 + 1-4 NB = 6.4868 1-4 EEL = -32.6310 VDWAALS = 3120.5532 + EELEC = -24812.9365 EHBOND = 0.0000 RESTRAINT = 1.4990 + EAMBER (non-restraint) = -21606.6271 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65653.2057 + Density = 0.9904 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 7 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8423 SC_EKtot= 0.0000 SC_EPtot = 0.8423 + SC_BOND= 0.0000 SC_ANGLE= 0.8410 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW 0.92231 1.00000 0.00000 -0.00000 +TI 2 vDW 0.49169 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= 0.9223 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.68956 1.00000 0.00000 -0.00000 +TI 2 Bond 430.98577 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.6896 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.60531 1.00000 0.00000 -0.00000 +TI 2 Angle 235.16275 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.6053 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.60550 1.00000 0.00000 -0.00000 +TI 2 Torsion 9.32800 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.6055 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.63096 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.63096 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.6310 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.48684 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.41448 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.4868 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 206.48885 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 498.43073 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 206.4888 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -116.26167 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 38.66888 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -116.2617 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 169.61160 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.91154 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02518 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01417 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21567.981114 +Energy at 0.0667 = -21565.064743 +Energy at 0.1333 = -21547.026484 +Energy at 0.2000 = -21504.771517 +Energy at 0.2667 = -21434.815793 +Energy at 0.3333 = -21338.238937 +Energy at 0.4000 = -21219.594596 +Energy at 0.4667 = -21086.000032 +Energy at 0.5333 = -20946.141576 +Energy at 0.6000 = -20809.295413 +Energy at 0.6667 = -20684.621712 +Energy at 0.7333 = -20580.306659 +Energy at 0.8000 = -20502.607386 +Energy at 0.8667 = -20454.529646 +Energy at 0.9333 = -20433.684723 +Energy at 1.0000 = -20430.294493 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 7200 TIME(PS) = 14.400 TEMP(K) = 300.23 PRESS = 0.0 + Etot = -17705.5002 EKtot = 3862.4809 EPtot = -21567.9811 + BOND = 5.5762 ANGLE = 100.3029 DIHED = 4.1522 + 1-4 NB = 7.3291 1-4 EEL = -33.3966 VDWAALS = 3114.1069 + EELEC = -24768.8040 EHBOND = 0.0000 RESTRAINT = 2.7522 + EAMBER (non-restraint) = -21570.7333 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65429.6592 + Density = 0.9938 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.1056 SC_EKtot= 0.0000 SC_EPtot = 1.1056 + SC_BOND= 0.0000 SC_ANGLE= 1.1044 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 7200 TIME(PS) = 14.400 TEMP(K) = 300.23 PRESS = 0.0 + Etot = -17705.5002 EKtot = 3862.4809 EPtot = -21567.9811 + BOND = 5.5762 ANGLE = 100.3029 DIHED = 4.1522 + 1-4 NB = 7.3291 1-4 EEL = -33.3966 VDWAALS = 3114.1069 + EELEC = -24768.8040 EHBOND = 0.0000 RESTRAINT = 2.7522 + EAMBER (non-restraint) = -21570.7333 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65429.6592 + Density = 0.9938 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.1056 SC_EKtot= 0.0000 SC_EPtot = 1.1056 + SC_BOND= 0.0000 SC_ANGLE= 1.1044 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -1.95186 1.00000 0.00000 -0.00000 +TI 2 vDW -2.40875 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -1.9519 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.57622 1.00000 0.00000 -0.00000 +TI 2 Bond 487.58200 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.5762 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.30292 1.00000 0.00000 -0.00000 +TI 2 Angle 215.10196 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.3029 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 4.15219 1.00000 0.00000 -0.00000 +TI 2 Torsion 4.44515 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 4.1522 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.39656 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.39656 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.3966 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 7.32910 1.00000 0.00000 -0.00000 +TI 2 VDW14 7.25836 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 7.3291 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 215.21173 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 497.06506 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 215.2117 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -104.93173 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 17.18612 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -104.9317 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 178.09453 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.87731 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02528 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01423 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21598.162984 +Energy at 0.0667 = -21595.323008 +Energy at 0.1333 = -21577.758406 +Energy at 0.2000 = -21536.621026 +Energy at 0.2667 = -21468.542576 +Energy at 0.3333 = -21374.621584 +Energy at 0.4000 = -21259.366316 +Energy at 0.4667 = -21129.809466 +Energy at 0.5333 = -20994.535163 +Energy at 0.6000 = -20862.704996 +Energy at 0.6667 = -20743.310365 +Energy at 0.7333 = -20644.220904 +Energy at 0.8000 = -20571.131508 +Energy at 0.8667 = -20526.331569 +Energy at 0.9333 = -20507.033725 +Energy at 1.0000 = -20503.903186 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 7400 TIME(PS) = 14.800 TEMP(K) = 303.03 PRESS = 0.0 + Etot = -17699.5991 EKtot = 3898.5639 EPtot = -21598.1630 + BOND = 7.0906 ANGLE = 95.7153 DIHED = 6.2006 + 1-4 NB = 6.8654 1-4 EEL = -33.1124 VDWAALS = 3291.7933 + EELEC = -24974.9518 EHBOND = 0.0000 RESTRAINT = 2.2362 + EAMBER (non-restraint) = -21600.3992 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65447.5776 + Density = 0.9935 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.1970 SC_EKtot= 0.0000 SC_EPtot = 1.1970 + SC_BOND= 0.0000 SC_ANGLE= 1.1958 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 7400 TIME(PS) = 14.800 TEMP(K) = 303.03 PRESS = 0.0 + Etot = -17699.5991 EKtot = 3898.5639 EPtot = -21598.1630 + BOND = 7.0906 ANGLE = 95.7153 DIHED = 6.2006 + 1-4 NB = 6.8654 1-4 EEL = -33.1124 VDWAALS = 3291.7933 + EELEC = -24974.9518 EHBOND = 0.0000 RESTRAINT = 2.2362 + EAMBER (non-restraint) = -21600.3992 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65447.5776 + Density = 0.9935 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.1970 SC_EKtot= 0.0000 SC_EPtot = 1.1970 + SC_BOND= 0.0000 SC_ANGLE= 1.1958 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -2.61932 1.00000 0.00000 -0.00000 +TI 2 vDW -3.01668 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -2.6193 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 7.09056 1.00000 0.00000 -0.00000 +TI 2 Bond 416.93722 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 7.0906 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 95.71528 1.00000 0.00000 -0.00000 +TI 2 Angle 225.59153 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 95.7153 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.20058 1.00000 0.00000 -0.00000 +TI 2 Torsion 7.63234 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.2006 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.11240 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.11240 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.1124 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.86537 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.78835 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.8654 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 218.51782 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 504.20566 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 218.5178 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -108.24651 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 46.41525 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -108.2465 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 168.82257 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.64224 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02506 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0251 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01410 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21502.259575 +Energy at 0.0667 = -21499.310161 +Energy at 0.1333 = -21481.069256 +Energy at 0.2000 = -21438.351664 +Energy at 0.2667 = -21367.669969 +Energy at 0.3333 = -21270.182966 +Energy at 0.4000 = -21150.594128 +Energy at 0.4667 = -21016.223839 +Energy at 0.5333 = -20875.986396 +Energy at 0.6000 = -20739.364779 +Energy at 0.6667 = -20615.628463 +Energy at 0.7333 = -20512.867170 +Energy at 0.8000 = -20436.958072 +Energy at 0.8667 = -20390.340333 +Energy at 0.9333 = -20370.228272 +Energy at 1.0000 = -20366.963496 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 7600 TIME(PS) = 15.200 TEMP(K) = 299.01 PRESS = 0.0 + Etot = -17655.4943 EKtot = 3846.7653 EPtot = -21502.2596 + BOND = 7.7577 ANGLE = 99.9599 DIHED = 9.2781 + 1-4 NB = 6.5440 1-4 EEL = -33.9158 VDWAALS = 3128.3971 + EELEC = -24724.0715 EHBOND = 0.0000 RESTRAINT = 3.7909 + EAMBER (non-restraint) = -21506.0504 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65509.7320 + Density = 0.9926 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6768 SC_EKtot= 0.0000 SC_EPtot = 0.6768 + SC_BOND= 0.0000 SC_ANGLE= 0.6756 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 7600 TIME(PS) = 15.200 TEMP(K) = 299.01 PRESS = 0.0 + Etot = -17655.4943 EKtot = 3846.7653 EPtot = -21502.2596 + BOND = 7.7577 ANGLE = 99.9599 DIHED = 9.2781 + 1-4 NB = 6.5440 1-4 EEL = -33.9158 VDWAALS = 3128.3971 + EELEC = -24724.0715 EHBOND = 0.0000 RESTRAINT = 3.7909 + EAMBER (non-restraint) = -21506.0504 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65509.7320 + Density = 0.9926 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6768 SC_EKtot= 0.0000 SC_EPtot = 0.6768 + SC_BOND= 0.0000 SC_ANGLE= 0.6756 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -11.56103 1.00000 0.00000 -0.00000 +TI 2 vDW -11.91481 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -11.5610 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 7.75771 1.00000 0.00000 -0.00000 +TI 2 Bond 498.22704 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 7.7577 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.95993 1.00000 0.00000 -0.00000 +TI 2 Angle 228.21643 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.9599 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 9.27813 1.00000 0.00000 -0.00000 +TI 2 Torsion 16.21214 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 9.2781 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.91576 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.91576 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.9158 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.54395 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.47364 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.5440 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 227.44334 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 496.82999 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 227.4433 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -84.22664 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 48.95529 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -84.2266 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 162.49756 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.17656 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02515 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01416 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21576.835462 +Energy at 0.0667 = -21573.834075 +Energy at 0.1333 = -21555.271487 +Energy at 0.2000 = -21511.798797 +Energy at 0.2667 = -21439.861890 +Energy at 0.3333 = -21340.630305 +Energy at 0.4000 = -21218.876332 +Energy at 0.4667 = -21082.032069 +Energy at 0.5333 = -20939.151140 +Energy at 0.6000 = -20799.871051 +Energy at 0.6667 = -20673.627831 +Energy at 0.7333 = -20568.686383 +Energy at 0.8000 = -20491.093421 +Energy at 0.8667 = -20443.405726 +Energy at 0.9333 = -20422.823197 +Energy at 1.0000 = -20419.481537 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 7800 TIME(PS) = 15.600 TEMP(K) = 300.08 PRESS = 0.0 + Etot = -17716.2670 EKtot = 3860.5684 EPtot = -21576.8355 + BOND = 7.5973 ANGLE = 106.7592 DIHED = 11.0238 + 1-4 NB = 4.3437 1-4 EEL = -33.8120 VDWAALS = 3129.7971 + EELEC = -24803.7607 EHBOND = 0.0000 RESTRAINT = 1.2161 + EAMBER (non-restraint) = -21578.0516 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65509.7320 + Density = 0.9926 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.2867 SC_EKtot= 0.0000 SC_EPtot = 0.2867 + SC_BOND= 0.0000 SC_ANGLE= 0.2855 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 7800 TIME(PS) = 15.600 TEMP(K) = 300.08 PRESS = 0.0 + Etot = -17716.2670 EKtot = 3860.5684 EPtot = -21576.8355 + BOND = 7.5973 ANGLE = 106.7592 DIHED = 11.0238 + 1-4 NB = 4.3437 1-4 EEL = -33.8120 VDWAALS = 3129.7971 + EELEC = -24803.7607 EHBOND = 0.0000 RESTRAINT = 1.2161 + EAMBER (non-restraint) = -21578.0516 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65509.7320 + Density = 0.9926 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.2867 SC_EKtot= 0.0000 SC_EPtot = 0.2867 + SC_BOND= 0.0000 SC_ANGLE= 0.2855 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -14.22126 1.00000 0.00000 -0.00000 +TI 2 vDW -14.62455 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -14.2213 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 7.59729 1.00000 0.00000 -0.00000 +TI 2 Bond 510.21624 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 7.5973 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 106.75920 1.00000 0.00000 -0.00000 +TI 2 Angle 234.45520 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 106.7592 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 11.02384 1.00000 0.00000 -0.00000 +TI 2 Torsion 13.91665 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 11.0238 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.81201 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.81201 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.8120 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 4.34374 1.00000 0.00000 -0.00000 +TI 2 VDW14 4.27502 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 4.3437 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 222.19751 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 493.34418 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 222.1975 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -97.05155 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 43.27731 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -97.0516 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 165.30370 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.96287 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02486 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0249 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01399 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21606.206275 +Energy at 0.0667 = -21603.332009 +Energy at 0.1333 = -21585.554833 +Energy at 0.2000 = -21543.915934 +Energy at 0.2667 = -21474.994293 +Energy at 0.3333 = -21379.875001 +Energy at 0.4000 = -21263.070210 +Energy at 0.4667 = -21131.610518 +Energy at 0.5333 = -20994.047340 +Energy at 0.6000 = -20859.467356 +Energy at 0.6667 = -20736.785419 +Energy at 0.7333 = -20633.930206 +Energy at 0.8000 = -20557.015596 +Energy at 0.8667 = -20509.171620 +Energy at 0.9333 = -20488.335248 +Energy at 1.0000 = -20484.939762 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 8000 TIME(PS) = 16.000 TEMP(K) = 291.36 PRESS = 0.0 + Etot = -17857.8877 EKtot = 3748.3186 EPtot = -21606.2063 + BOND = 11.2195 ANGLE = 104.1321 DIHED = 12.3558 + 1-4 NB = 5.6722 1-4 EEL = -32.6140 VDWAALS = 3098.0155 + EELEC = -24807.3743 EHBOND = 0.0000 RESTRAINT = 2.3869 + EAMBER (non-restraint) = -21608.5932 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65379.8973 + Density = 0.9945 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4640 SC_EKtot= 0.0000 SC_EPtot = 0.4640 + SC_BOND= 0.0000 SC_ANGLE= 0.4628 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 8000 TIME(PS) = 16.000 TEMP(K) = 291.36 PRESS = 0.0 + Etot = -17857.8877 EKtot = 3748.3186 EPtot = -21606.2063 + BOND = 11.2195 ANGLE = 104.1321 DIHED = 12.3558 + 1-4 NB = 5.6722 1-4 EEL = -32.6140 VDWAALS = 3098.0155 + EELEC = -24807.3743 EHBOND = 0.0000 RESTRAINT = 2.3869 + EAMBER (non-restraint) = -21608.5932 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65379.8973 + Density = 0.9945 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 8 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.4640 SC_EKtot= 0.0000 SC_EPtot = 0.4640 + SC_BOND= 0.0000 SC_ANGLE= 0.4628 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -1.91705 1.00000 0.00000 -0.00000 +TI 2 vDW -2.40163 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -1.9171 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 11.21951 1.00000 0.00000 -0.00000 +TI 2 Bond 452.17676 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 11.2195 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 104.13209 1.00000 0.00000 -0.00000 +TI 2 Angle 233.75245 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 104.1321 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 12.35585 1.00000 0.00000 -0.00000 +TI 2 Torsion 12.46827 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 12.3558 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.61404 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.61404 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.6140 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.67222 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.60411 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.6722 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 217.27467 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 480.05579 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 217.2747 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -117.96497 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 43.91300 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -117.9650 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 167.04208 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.81414 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02519 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01418 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21643.840817 +Energy at 0.0667 = -21640.792145 +Energy at 0.1333 = -21621.936432 +Energy at 0.2000 = -21577.772427 +Energy at 0.2667 = -21504.674990 +Energy at 0.3333 = -21403.801936 +Energy at 0.4000 = -21279.950206 +Energy at 0.4667 = -21140.591430 +Energy at 0.5333 = -20994.808845 +Energy at 0.6000 = -20852.237384 +Energy at 0.6667 = -20722.285590 +Energy at 0.7333 = -20613.250338 +Energy at 0.8000 = -20531.496739 +Energy at 0.8667 = -20480.401153 +Energy at 0.9333 = -20458.042935 +Energy at 1.0000 = -20454.391167 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 8200 TIME(PS) = 16.400 TEMP(K) = 297.36 PRESS = 0.0 + Etot = -17818.3447 EKtot = 3825.4961 EPtot = -21643.8408 + BOND = 6.9819 ANGLE = 104.1133 DIHED = 9.4750 + 1-4 NB = 6.6643 1-4 EEL = -34.2403 VDWAALS = 3052.2899 + EELEC = -24789.6375 EHBOND = 0.0000 RESTRAINT = 0.5126 + EAMBER (non-restraint) = -21644.3534 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65379.8973 + Density = 0.9945 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6352 SC_EKtot= 0.0000 SC_EPtot = 0.6352 + SC_BOND= 0.0000 SC_ANGLE= 0.6340 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 8200 TIME(PS) = 16.400 TEMP(K) = 297.36 PRESS = 0.0 + Etot = -17818.3447 EKtot = 3825.4961 EPtot = -21643.8408 + BOND = 6.9819 ANGLE = 104.1133 DIHED = 9.4750 + 1-4 NB = 6.6643 1-4 EEL = -34.2403 VDWAALS = 3052.2899 + EELEC = -24789.6375 EHBOND = 0.0000 RESTRAINT = 0.5126 + EAMBER (non-restraint) = -21644.3534 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65379.8973 + Density = 0.9945 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6352 SC_EKtot= 0.0000 SC_EPtot = 0.6352 + SC_BOND= 0.0000 SC_ANGLE= 0.6340 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -6.17352 1.00000 0.00000 -0.00000 +TI 2 vDW -6.58165 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -6.1735 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.98186 1.00000 0.00000 -0.00000 +TI 2 Bond 513.36491 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.9819 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 104.11334 1.00000 0.00000 -0.00000 +TI 2 Angle 227.26789 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 104.1133 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 9.47498 1.00000 0.00000 -0.00000 +TI 2 Torsion 11.35313 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 9.4750 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.24028 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.24028 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.2403 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.66434 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.58782 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.6643 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 213.34674 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 485.73352 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 213.3467 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -112.25238 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 40.79150 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -112.2524 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 173.43303 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -48.57218 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02526 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01422 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21599.457455 +Energy at 0.0667 = -21596.582032 +Energy at 0.1333 = -21578.797704 +Energy at 0.2000 = -21537.142086 +Energy at 0.2667 = -21468.192891 +Energy at 0.3333 = -21373.035968 +Energy at 0.4000 = -21256.186217 +Energy at 0.4667 = -21124.679598 +Energy at 0.5333 = -20987.076897 +Energy at 0.6000 = -20852.480255 +Energy at 0.6667 = -20729.827496 +Energy at 0.7333 = -20627.073057 +Energy at 0.8000 = -20550.335735 +Energy at 0.8667 = -20502.688866 +Energy at 0.9333 = -20481.971768 +Energy at 1.0000 = -20478.598183 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 8400 TIME(PS) = 16.800 TEMP(K) = 294.52 PRESS = 0.0 + Etot = -17810.4801 EKtot = 3788.9774 EPtot = -21599.4575 + BOND = 6.6593 ANGLE = 100.0677 DIHED = 9.5629 + 1-4 NB = 5.4408 1-4 EEL = -34.5228 VDWAALS = 3165.6996 + EELEC = -24854.7270 EHBOND = 0.0000 RESTRAINT = 2.3621 + EAMBER (non-restraint) = -21601.8196 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65223.0429 + Density = 0.9969 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9522 SC_EKtot= 0.0000 SC_EPtot = 0.9522 + SC_BOND= 0.0000 SC_ANGLE= 0.9510 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 8400 TIME(PS) = 16.800 TEMP(K) = 294.52 PRESS = 0.0 + Etot = -17810.4801 EKtot = 3788.9774 EPtot = -21599.4575 + BOND = 6.6593 ANGLE = 100.0677 DIHED = 9.5629 + 1-4 NB = 5.4408 1-4 EEL = -34.5228 VDWAALS = 3165.6996 + EELEC = -24854.7270 EHBOND = 0.0000 RESTRAINT = 2.3621 + EAMBER (non-restraint) = -21601.8196 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65223.0429 + Density = 0.9969 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9522 SC_EKtot= 0.0000 SC_EPtot = 0.9522 + SC_BOND= 0.0000 SC_ANGLE= 0.9510 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -6.70298 1.00000 0.00000 -0.00000 +TI 2 vDW -7.12810 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -6.7030 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.65934 1.00000 0.00000 -0.00000 +TI 2 Bond 448.56266 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.6593 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.06770 1.00000 0.00000 -0.00000 +TI 2 Angle 215.56612 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.0677 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 9.56286 1.00000 0.00000 -0.00000 +TI 2 Torsion 10.03597 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 9.5629 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.52283 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.52283 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.5228 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.44078 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.36636 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.4408 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 208.45816 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 492.84247 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 208.4582 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -113.37370 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 39.86348 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -113.3737 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 169.72514 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -48.26506 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02531 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01424 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21630.110564 +Energy at 0.0667 = -21626.996871 +Energy at 0.1333 = -21607.738682 +Energy at 0.2000 = -21562.629673 +Energy at 0.2667 = -21487.960312 +Energy at 0.3333 = -21384.899311 +Energy at 0.4000 = -21258.323414 +Energy at 0.4667 = -21115.829631 +Energy at 0.5333 = -20966.646332 +Energy at 0.6000 = -20820.553041 +Energy at 0.6667 = -20687.111958 +Energy at 0.7333 = -20574.834259 +Energy at 0.8000 = -20490.416728 +Energy at 0.8667 = -20437.579894 +Energy at 0.9333 = -20414.460791 +Energy at 1.0000 = -20410.685967 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 8600 TIME(PS) = 17.200 TEMP(K) = 294.22 PRESS = 0.0 + Etot = -17844.9784 EKtot = 3785.1322 EPtot = -21630.1106 + BOND = 6.8240 ANGLE = 99.3335 DIHED = 10.7466 + 1-4 NB = 4.6772 1-4 EEL = -32.9294 VDWAALS = 3154.0487 + EELEC = -24875.0620 EHBOND = 0.0000 RESTRAINT = 2.2509 + EAMBER (non-restraint) = -21632.3615 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65223.0429 + Density = 0.9969 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9371 SC_EKtot= 0.0000 SC_EPtot = 0.9371 + SC_BOND= 0.0000 SC_ANGLE= 0.9359 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 8600 TIME(PS) = 17.200 TEMP(K) = 294.22 PRESS = 0.0 + Etot = -17844.9784 EKtot = 3785.1322 EPtot = -21630.1106 + BOND = 6.8240 ANGLE = 99.3335 DIHED = 10.7466 + 1-4 NB = 4.6772 1-4 EEL = -32.9294 VDWAALS = 3154.0487 + EELEC = -24875.0620 EHBOND = 0.0000 RESTRAINT = 2.2509 + EAMBER (non-restraint) = -21632.3615 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65223.0429 + Density = 0.9969 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9371 SC_EKtot= 0.0000 SC_EPtot = 0.9371 + SC_BOND= 0.0000 SC_ANGLE= 0.9359 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW 0.58422 1.00000 0.00000 -0.00000 +TI 2 vDW 0.17379 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= 0.5842 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.82399 1.00000 0.00000 -0.00000 +TI 2 Bond 475.96206 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.8240 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.33349 1.00000 0.00000 -0.00000 +TI 2 Angle 230.53263 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.3335 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 10.74656 1.00000 0.00000 -0.00000 +TI 2 Torsion 9.64646 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 10.7466 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.92940 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.92940 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.9294 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 4.67717 1.00000 0.00000 -0.00000 +TI 2 VDW14 4.60386 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 4.6772 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 211.98656 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 510.76099 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 211.9866 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -122.53607 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 56.98861 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -122.5361 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 175.21160 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.73797 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02533 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0253 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01426 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21528.066304 +Energy at 0.0667 = -21524.986324 +Energy at 0.1333 = -21505.935554 +Energy at 0.2000 = -21461.304824 +Energy at 0.2667 = -21387.402374 +Energy at 0.3333 = -21285.343838 +Energy at 0.4000 = -21159.897219 +Energy at 0.4667 = -21018.516230 +Energy at 0.5333 = -20870.283816 +Energy at 0.6000 = -20724.875270 +Energy at 0.6667 = -20591.833191 +Energy at 0.7333 = -20479.747158 +Energy at 0.8000 = -20395.431240 +Energy at 0.8667 = -20342.666760 +Energy at 0.9333 = -20319.586645 +Energy at 1.0000 = -20315.818759 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 8800 TIME(PS) = 17.600 TEMP(K) = 298.23 PRESS = 0.0 + Etot = -17691.2931 EKtot = 3836.7732 EPtot = -21528.0663 + BOND = 3.0823 ANGLE = 103.1940 DIHED = 6.2036 + 1-4 NB = 5.9870 1-4 EEL = -31.6521 VDWAALS = 3046.0042 + EELEC = -24666.4332 EHBOND = 0.0000 RESTRAINT = 5.5479 + EAMBER (non-restraint) = -21533.6142 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65223.0429 + Density = 0.9969 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6870 SC_EKtot= 0.0000 SC_EPtot = 0.6870 + SC_BOND= 0.0000 SC_ANGLE= 0.6858 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 8800 TIME(PS) = 17.600 TEMP(K) = 298.23 PRESS = 0.0 + Etot = -17691.2931 EKtot = 3836.7732 EPtot = -21528.0663 + BOND = 3.0823 ANGLE = 103.1940 DIHED = 6.2036 + 1-4 NB = 5.9870 1-4 EEL = -31.6521 VDWAALS = 3046.0042 + EELEC = -24666.4332 EHBOND = 0.0000 RESTRAINT = 5.5479 + EAMBER (non-restraint) = -21533.6142 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65223.0429 + Density = 0.9969 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.6870 SC_EKtot= 0.0000 SC_EPtot = 0.6870 + SC_BOND= 0.0000 SC_ANGLE= 0.6858 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -6.64177 1.00000 0.00000 -0.00000 +TI 2 vDW -7.10737 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -6.6418 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 3.08232 1.00000 0.00000 -0.00000 +TI 2 Bond 459.97322 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 3.0823 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 103.19397 1.00000 0.00000 -0.00000 +TI 2 Angle 223.52039 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 103.1940 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.20361 1.00000 0.00000 -0.00000 +TI 2 Torsion 7.19187 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.2036 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -31.65212 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -31.65212 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -31.6521 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.98703 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.91374 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.9870 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 216.55273 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 541.92462 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 216.5527 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -114.25132 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 40.28687 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -114.2513 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 181.67164 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.33365 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02503 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01409 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21631.744031 +Energy at 0.0667 = -21628.743908 +Energy at 0.1333 = -21610.187261 +Energy at 0.2000 = -21566.715333 +Energy at 0.2667 = -21494.735782 +Energy at 0.3333 = -21395.342592 +Energy at 0.4000 = -21273.192371 +Energy at 0.4667 = -21135.565281 +Energy at 0.5333 = -20991.340386 +Energy at 0.6000 = -20849.990755 +Energy at 0.6667 = -20720.874305 +Energy at 0.7333 = -20612.403155 +Energy at 0.8000 = -20531.158344 +Energy at 0.8667 = -20480.580274 +Energy at 0.9333 = -20458.550386 +Energy at 1.0000 = -20454.960604 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 9000 TIME(PS) = 18.000 TEMP(K) = 301.16 PRESS = 0.0 + Etot = -17757.3316 EKtot = 3874.4124 EPtot = -21631.7440 + BOND = 6.0036 ANGLE = 103.4136 DIHED = 6.0505 + 1-4 NB = 6.0971 1-4 EEL = -35.9602 VDWAALS = 3171.4451 + EELEC = -24891.4215 EHBOND = 0.0000 RESTRAINT = 2.6278 + EAMBER (non-restraint) = -21634.3719 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64984.7206 + Density = 1.0006 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.5826 SC_EKtot= 0.0000 SC_EPtot = 0.5826 + SC_BOND= 0.0000 SC_ANGLE= 0.5814 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 9000 TIME(PS) = 18.000 TEMP(K) = 301.16 PRESS = 0.0 + Etot = -17757.3316 EKtot = 3874.4124 EPtot = -21631.7440 + BOND = 6.0036 ANGLE = 103.4136 DIHED = 6.0505 + 1-4 NB = 6.0971 1-4 EEL = -35.9602 VDWAALS = 3171.4451 + EELEC = -24891.4215 EHBOND = 0.0000 RESTRAINT = 2.6278 + EAMBER (non-restraint) = -21634.3719 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 64984.7206 + Density = 1.0006 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 9 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.5826 SC_EKtot= 0.0000 SC_EPtot = 0.5826 + SC_BOND= 0.0000 SC_ANGLE= 0.5814 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -8.61500 1.00000 0.00000 -0.00000 +TI 2 vDW -9.07132 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -8.6150 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 6.00360 1.00000 0.00000 -0.00000 +TI 2 Bond 480.89540 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 6.0036 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 103.41358 1.00000 0.00000 -0.00000 +TI 2 Angle 214.65677 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 103.4136 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.05052 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.53589 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.0505 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -35.96025 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -35.96025 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -35.9602 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.09710 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.02004 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.0971 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 218.88715 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 519.82727 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 218.8871 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -103.83859 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 39.77034 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -103.8386 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 183.18254 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -49.75498 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02524 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01420 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21582.573749 +Energy at 0.0667 = -21579.835776 +Energy at 0.1333 = -21562.900978 +Energy at 0.2000 = -21523.231122 +Energy at 0.2667 = -21457.555814 +Energy at 0.3333 = -21366.889024 +Energy at 0.4000 = -21255.505026 +Energy at 0.4667 = -21130.082129 +Energy at 0.5333 = -20998.767506 +Energy at 0.6000 = -20870.257742 +Energy at 0.6667 = -20753.139954 +Energy at 0.7333 = -20655.096729 +Energy at 0.8000 = -20582.022282 +Energy at 0.8667 = -20536.778853 +Energy at 0.9333 = -20517.155036 +Energy at 1.0000 = -20513.962930 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 9200 TIME(PS) = 18.400 TEMP(K) = 297.13 PRESS = 0.0 + Etot = -17760.0083 EKtot = 3822.5654 EPtot = -21582.5737 + BOND = 8.0887 ANGLE = 103.0470 DIHED = 2.5469 + 1-4 NB = 7.1311 1-4 EEL = -33.1523 VDWAALS = 3115.1467 + EELEC = -24787.7504 EHBOND = 0.0000 RESTRAINT = 2.3685 + EAMBER (non-restraint) = -21584.9423 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65541.7651 + Density = 0.9921 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9984 SC_EKtot= 0.0000 SC_EPtot = 0.9984 + SC_BOND= 0.0000 SC_ANGLE= 0.9972 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 9200 TIME(PS) = 18.400 TEMP(K) = 297.13 PRESS = 0.0 + Etot = -17760.0083 EKtot = 3822.5654 EPtot = -21582.5737 + BOND = 8.0887 ANGLE = 103.0470 DIHED = 2.5469 + 1-4 NB = 7.1311 1-4 EEL = -33.1523 VDWAALS = 3115.1467 + EELEC = -24787.7504 EHBOND = 0.0000 RESTRAINT = 2.3685 + EAMBER (non-restraint) = -21584.9423 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65541.7651 + Density = 0.9921 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.9984 SC_EKtot= 0.0000 SC_EPtot = 0.9984 + SC_BOND= 0.0000 SC_ANGLE= 0.9972 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -1.19015 1.00000 0.00000 -0.00000 +TI 2 vDW -1.62002 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -1.1901 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.08871 1.00000 0.00000 -0.00000 +TI 2 Bond 421.11326 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.0887 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 103.04698 1.00000 0.00000 -0.00000 +TI 2 Angle 224.74621 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 103.0470 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 2.54687 1.00000 0.00000 -0.00000 +TI 2 Torsion 2.68245 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 2.5469 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.15227 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.15227 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.1523 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 7.13110 1.00000 0.00000 -0.00000 +TI 2 VDW14 7.05865 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 7.1311 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 216.33487 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 498.50870 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 216.3349 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -98.76838 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 23.67456 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -98.7684 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 173.37484 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.27862 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02502 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01408 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21543.474177 +Energy at 0.0667 = -21540.576706 +Energy at 0.1333 = -21522.655427 +Energy at 0.2000 = -21480.675040 +Energy at 0.2667 = -21411.175207 +Energy at 0.3333 = -21315.228654 +Energy at 0.4000 = -21197.354068 +Energy at 0.4667 = -21064.602796 +Energy at 0.5333 = -20925.556552 +Energy at 0.6000 = -20789.337446 +Energy at 0.6667 = -20664.904586 +Energy at 0.7333 = -20560.263572 +Energy at 0.8000 = -20481.695540 +Energy at 0.8667 = -20432.611127 +Energy at 0.9333 = -20411.166340 +Energy at 1.0000 = -20407.667156 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 9400 TIME(PS) = 18.800 TEMP(K) = 297.00 PRESS = 0.0 + Etot = -17722.5359 EKtot = 3820.9383 EPtot = -21543.4742 + BOND = 8.7589 ANGLE = 103.2763 DIHED = 7.4679 + 1-4 NB = 6.3039 1-4 EEL = -34.0500 VDWAALS = 3168.3691 + EELEC = -24805.6208 EHBOND = 0.0000 RESTRAINT = 2.0204 + EAMBER (non-restraint) = -21545.4946 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65541.7651 + Density = 0.9921 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8286 SC_EKtot= 0.0000 SC_EPtot = 0.8286 + SC_BOND= 0.0000 SC_ANGLE= 0.8274 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 9400 TIME(PS) = 18.800 TEMP(K) = 297.00 PRESS = 0.0 + Etot = -17722.5359 EKtot = 3820.9383 EPtot = -21543.4742 + BOND = 8.7589 ANGLE = 103.2763 DIHED = 7.4679 + 1-4 NB = 6.3039 1-4 EEL = -34.0500 VDWAALS = 3168.3691 + EELEC = -24805.6208 EHBOND = 0.0000 RESTRAINT = 2.0204 + EAMBER (non-restraint) = -21545.4946 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65541.7651 + Density = 0.9921 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.8286 SC_EKtot= 0.0000 SC_EPtot = 0.8286 + SC_BOND= 0.0000 SC_ANGLE= 0.8274 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -2.70123 1.00000 0.00000 -0.00000 +TI 2 vDW -3.13268 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -2.7012 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 8.75892 1.00000 0.00000 -0.00000 +TI 2 Bond 444.96080 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 8.7589 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 103.27634 1.00000 0.00000 -0.00000 +TI 2 Angle 227.45361 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 103.2763 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 7.46791 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.89291 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 7.4679 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -34.04998 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -34.04998 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -34.0500 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.30386 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.23014 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.3039 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 220.20454 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 501.55261 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 220.2045 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -110.47166 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 46.42558 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -110.4717 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 176.04296 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.89245 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02478 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01395 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21468.395343 +Energy at 0.0667 = -21465.442448 +Energy at 0.1333 = -21447.178927 +Energy at 0.2000 = -21404.400618 +Energy at 0.2667 = -21333.591633 +Energy at 0.3333 = -21235.862297 +Energy at 0.4000 = -21115.835482 +Energy at 0.4667 = -20980.702703 +Energy at 0.5333 = -20839.180985 +Energy at 0.6000 = -20700.476637 +Energy at 0.6667 = -20573.553898 +Energy at 0.7333 = -20466.380926 +Energy at 0.8000 = -20385.326839 +Energy at 0.8667 = -20334.214453 +Energy at 0.9333 = -20311.708699 +Energy at 1.0000 = -20308.023786 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 9600 TIME(PS) = 19.200 TEMP(K) = 299.94 PRESS = 0.0 + Etot = -17609.6533 EKtot = 3858.7421 EPtot = -21468.3953 + BOND = 12.1936 ANGLE = 100.6334 DIHED = 6.5981 + 1-4 NB = 6.5604 1-4 EEL = -33.1956 VDWAALS = 3035.0510 + EELEC = -24599.2427 EHBOND = 0.0000 RESTRAINT = 3.0065 + EAMBER (non-restraint) = -21471.4019 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65541.7651 + Density = 0.9921 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.3074 SC_EKtot= 0.0000 SC_EPtot = 1.3074 + SC_BOND= 0.0000 SC_ANGLE= 1.3062 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 9600 TIME(PS) = 19.200 TEMP(K) = 299.94 PRESS = 0.0 + Etot = -17609.6533 EKtot = 3858.7421 EPtot = -21468.3953 + BOND = 12.1936 ANGLE = 100.6334 DIHED = 6.5981 + 1-4 NB = 6.5604 1-4 EEL = -33.1956 VDWAALS = 3035.0510 + EELEC = -24599.2427 EHBOND = 0.0000 RESTRAINT = 3.0065 + EAMBER (non-restraint) = -21471.4019 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65541.7651 + Density = 0.9921 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 1.3074 SC_EKtot= 0.0000 SC_EPtot = 1.3074 + SC_BOND= 0.0000 SC_ANGLE= 1.3062 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -11.70152 1.00000 0.00000 -0.00000 +TI 2 vDW -12.10566 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -11.7015 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 12.19360 1.00000 0.00000 -0.00000 +TI 2 Bond 507.65803 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 12.1936 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.63336 1.00000 0.00000 -0.00000 +TI 2 Angle 226.51442 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.6334 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 6.59807 1.00000 0.00000 -0.00000 +TI 2 Torsion 5.66853 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 6.5981 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.19564 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.19564 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.1956 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.56044 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.48817 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.5604 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 227.98608 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 498.89011 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 227.9861 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -94.95899 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 37.15499 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -94.9590 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 170.10271 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -47.64263 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02485 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0248 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01399 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21525.190874 +Energy at 0.0667 = -21522.213889 +Energy at 0.1333 = -21503.800364 +Energy at 0.2000 = -21460.663809 +Energy at 0.2667 = -21389.239951 +Energy at 0.3333 = -21290.615277 +Energy at 0.4000 = -21169.412210 +Energy at 0.4667 = -21032.856852 +Energy at 0.5333 = -20889.760809 +Energy at 0.6000 = -20749.522462 +Energy at 0.6667 = -20621.424501 +Energy at 0.7333 = -20513.815515 +Energy at 0.8000 = -20433.232825 +Energy at 0.8667 = -20383.086738 +Energy at 0.9333 = -20361.253914 +Energy at 1.0000 = -20357.696920 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 9800 TIME(PS) = 19.600 TEMP(K) = 299.47 PRESS = 0.0 + Etot = -17672.4919 EKtot = 3852.6989 EPtot = -21525.1909 + BOND = 5.2384 ANGLE = 100.5930 DIHED = 5.6786 + 1-4 NB = 6.7127 1-4 EEL = -32.0073 VDWAALS = 3127.8126 + EELEC = -24743.8929 EHBOND = 0.0000 RESTRAINT = 4.6740 + EAMBER (non-restraint) = -21529.8649 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65474.3783 + Density = 0.9931 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7378 SC_EKtot= 0.0000 SC_EPtot = 0.7378 + SC_BOND= 0.0000 SC_ANGLE= 0.7366 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 9800 TIME(PS) = 19.600 TEMP(K) = 299.47 PRESS = 0.0 + Etot = -17672.4919 EKtot = 3852.6989 EPtot = -21525.1909 + BOND = 5.2384 ANGLE = 100.5930 DIHED = 5.6786 + 1-4 NB = 6.7127 1-4 EEL = -32.0073 VDWAALS = 3127.8126 + EELEC = -24743.8929 EHBOND = 0.0000 RESTRAINT = 4.6740 + EAMBER (non-restraint) = -21529.8649 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65474.3783 + Density = 0.9931 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.7378 SC_EKtot= 0.0000 SC_EPtot = 0.7378 + SC_BOND= 0.0000 SC_ANGLE= 0.7366 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW 4.75667 1.00000 0.00000 -0.00000 +TI 2 vDW 4.29160 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= 4.7567 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 5.23839 1.00000 0.00000 -0.00000 +TI 2 Bond 473.21874 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 5.2384 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 100.59299 1.00000 0.00000 -0.00000 +TI 2 Angle 232.13776 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 100.5930 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 5.67856 1.00000 0.00000 -0.00000 +TI 2 Torsion 8.16074 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 5.6786 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -32.00727 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -32.00727 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -32.0073 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 6.71273 1.00000 0.00000 -0.00000 +TI 2 VDW14 6.64530 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 6.7127 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 216.13116 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 501.85001 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 216.1312 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -114.01079 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 21.17068 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -114.0108 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 177.53447 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -45.49507 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02523 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0252 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01420 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + +MBAR Energy analysis: +Energy at 0.0000 = -21531.180954 +Energy at 0.0667 = -21528.134858 +Energy at 0.1333 = -21509.295164 +Energy at 0.2000 = -21465.169467 +Energy at 0.2667 = -21392.139200 +Energy at 0.3333 = -21291.372127 +Energy at 0.4000 = -21167.688707 +Energy at 0.4667 = -21028.613338 +Energy at 0.5333 = -20883.331577 +Energy at 0.6000 = -20741.646872 +Energy at 0.6667 = -20613.185322 +Energy at 0.7333 = -20506.395345 +Energy at 0.8000 = -20427.453443 +Energy at 0.8667 = -20378.953533 +Energy at 0.9333 = -20358.026026 +Energy at 1.0000 = -20354.628722 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 303.01 PRESS = 0.0 + Etot = -17632.9022 EKtot = 3898.2788 EPtot = -21531.1810 + BOND = 9.7184 ANGLE = 99.4332 DIHED = 7.9961 + 1-4 NB = 5.5397 1-4 EEL = -33.3447 VDWAALS = 3023.7942 + EELEC = -24649.3495 EHBOND = 0.0000 RESTRAINT = 5.0317 + EAMBER (non-restraint) = -21536.2126 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65724.2169 + Density = 0.9893 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.5302 SC_EKtot= 0.0000 SC_EPtot = 0.5302 + SC_BOND= 0.0000 SC_ANGLE= 0.5290 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 2 + + + NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 303.01 PRESS = 0.0 + Etot = -17632.9022 EKtot = 3898.2788 EPtot = -21531.1810 + BOND = 9.7184 ANGLE = 99.4332 DIHED = 7.9961 + 1-4 NB = 5.5397 1-4 EEL = -33.3447 VDWAALS = 3023.7942 + EELEC = -24649.3495 EHBOND = 0.0000 RESTRAINT = 5.0317 + EAMBER (non-restraint) = -21536.2126 + EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 65724.2169 + Density = 0.9893 + TEMP0 = 298.0000 REPNUM = 1 EXCHANGE# = 10 + ------------------------------------------------------------------------------ + + Softcore part of the system: 3 atoms, TEMP(K) = 0.00 + SC_Etot= 0.5302 SC_EKtot= 0.0000 SC_EPtot = 0.5302 + SC_BOND= 0.0000 SC_ANGLE= 0.5290 SC_DIHED = 0.0012 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Detailed TI info at lambda= 0.0000000000000000 +Region H W dH/dl dW/dl +TI 1 vDW -7.83344 1.00000 0.00000 -0.00000 +TI 2 vDW -8.24040 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW H= -7.8334 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Bond 9.71837 1.00000 0.00000 -0.00000 +TI 2 Bond 479.73061 0.00000 0.00000 0.00000 +lambda = 0.000 : Bond H= 9.7184 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Angle 99.43321 1.00000 0.00000 -0.00000 +TI 2 Angle 222.56157 0.00000 0.00000 0.00000 +lambda = 0.000 : Angle H= 99.4332 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Torsion 7.99610 1.00000 0.00000 -0.00000 +TI 2 Torsion 7.24618 0.00000 0.00000 0.00000 +lambda = 0.000 : Torsion H= 7.9961 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-CC -33.34468 1.00000 0.00000 -0.00000 +TI 2 EE14-CC -33.34468 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-CC H= -33.3447 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 VDW14 5.53967 1.00000 0.00000 -0.00000 +TI 2 VDW14 5.46805 0.00000 0.00000 0.00000 +lambda = 0.000 : VDW14 H= 5.5397 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-Rec 215.27290 1.00000 0.00000 -0.00000 +TI 2 Elec-Rec 524.26910 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-Rec H= 215.2729 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-CC -108.29791 1.00000 0.00000 -0.00000 +TI 2 Elec-CC 42.49073 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-CC H= -108.2979 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Elec-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 Elec-SC 174.81428 0.00000 0.00000 0.00000 +lambda = 0.000 : Elec-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 EE14-SC 0.00000 1.00000 0.00000 -0.00000 +TI 2 EE14-SC -46.25059 0.00000 0.00000 0.00000 +lambda = 0.000 : EE14-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-Rec -0.02495 1.00000 0.00000 -0.00000 +TI 2 Self-Rec -0.00000 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-Rec H= -0.0250 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 Self-SC -0.00000 1.00000 0.00000 -0.00000 +TI 2 Self-SC -41.56967 0.00000 0.00000 0.00000 +lambda = 0.000 : Self-SC H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +TI 1 vDW-Corr 0.00000 1.00000 0.00000 -0.00000 +TI 2 vDW-Corr -0.01404 0.00000 0.00000 0.00000 +lambda = 0.000 : vDW-Corr H= 0.0000 dU/dL: L= 0.0000 NL= 0.0000 Tot= 0.00000 + ------------------------------------------------------------------------ +lambda = 0.000 : Total dU/dl: 0.000000 L: 0.00000 NL: 0.00000 PI: 0.00000 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines, Average for All Tasks: +| +| Routine Sec % +| ------------------------------ +| DataDistrib 0.03 0.03 +| Nonbond 55.74 57.35 +| Bond 0.00 0.00 +| Angle 0.00 0.00 +| Dihedral 0.00 0.00 +| Shake 0.08 0.09 +| RunMD 38.47 39.58 +| Other 2.88 2.96 +| ------------------------------ +| Total 97.21 + +| PME Nonbond Pairlist CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.00 +| Build List 0.00 0.00 +| --------------------------------- +| Total 0.00 0.00 + +| PME Direct Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.00 0.00 +| Exclude Masked 0.00 0.00 +| Other 0.03 0.04 +| --------------------------------- +| Total 0.03 0.04 + +| PME Reciprocal Force CPU Time, Average for All Tasks: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.00 0.00 +| Grid Charges 0.00 0.00 +| Scalar Sum 0.00 0.00 +| Gradient Sum 0.00 0.00 +| FFT 0.00 0.00 +| --------------------------------- +| Total 0.00 0.00 + +| PME Load Balancing CPU Time, Average for All Tasks: +| +| Routine Sec % +| ------------------------------------ +| Atom Reassign 0.00 0.00 +| Image Reassign 0.00 0.00 +| FFT Reassign 0.00 0.00 +| ------------------------------------ +| Total 0.00 0.00 + +| Final Performance Info: +| ----------------------------------------------------- +| Average timings for last 3600 steps: +| Elapsed(s) = 34.94 Per Step(ms) = 9.70 +| ns/day = 17.81 seconds/ns = 4852.24 +| +| Average timings for all steps: +| Elapsed(s) = 97.17 Per Step(ms) = 9.72 +| ns/day = 17.78 seconds/ns = 4858.48 +| ----------------------------------------------------- + +| Master Setup CPU time: 3.01 seconds +| Master NonSetup CPU time: 97.21 seconds +| Master Total CPU time: 100.22 seconds 0.03 hours + +| Master Setup wall time: 4 seconds +| Master NonSetup wall time: 97 seconds +| Master Total wall time: 101 seconds 0.03 hours diff --git a/tests/output/amber_fep_min.out b/tests/output/amber_fep_min.out new file mode 100644 index 000000000..ab624de02 --- /dev/null +++ b/tests/output/amber_fep_min.out @@ -0,0 +1,2059 @@ + + ------------------------------------------------------- + Amber 20 PMEMD 2020 + ------------------------------------------------------- + +| PMEMD implementation of SANDER, Release 18 + +| Executable base on git commit: 5582ead046263fa35196b75ad7a34d5162126b1e +| Compiled date/time: Thu Dec 22 17:21:43 2022 +| Compiled on: rioja-rutgers-edu +| Compiled by: taisung + +| Run on 04/26/2023 at 09:32:12 + +| Executable path: /exs/shared/software/amber/gpu/amber-drug-discovery-boost/bin/pmemd.cuda +| Working directory: /tmp/tmpa3w_fsqn +| Hostname: gaia-login0 + + [-O]verwriting output + +File Assignments: +| MDIN: amber.cfg +| MDOUT: amber.out +| INPCRD: amber.rst7 +| PARM: amber.prm7 +| RESTRT: amber.crd +| REFC: refc +| MDVEL: mdvel +| MDEN: mden +| MDCRD: mdcrd +| MDINFO: amber.nrg +| MDFRC: mdfrc + + + Here is the input file: + +FreeEnergyMinimisation +&cntrl + ntpr=200, + ntxo=2, + irest=0, + ntx=1, + imin=1, + ntmin=2, + maxcyc=10000, + ncyc=1000, + cut=8.0, + iwrap=1, + icfe=1, + ifsc=1, + ntf=1, + mbar_states=11, + mbar_lambda=0.00000, 0.10000, 0.20000, 0.30000, 0.40000, 0.50000, 0.60000, 0 + clambda=0.00000, + timask1="@6481-6485", + timask2="@6486-6491", + scmask1="", + scmask2="@6491", + noshakemask="", +/ + + +Note: ig = -1. Setting random seed to 54474 based on wallclock time in + microseconds. +| irandom = 1, using AMBER's internal random number generator (default). + +|--------------------- INFORMATION ---------------------- +| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE. +| Version 18.0.0 +| +| 03/25/2018 +| +| Implementation by: +| Ross C. Walker (SDSC) +| Scott Le Grand (nVIDIA) +| +| Version 18 performance extensions by: +| David Cerutti (Rutgers) +| +| Precision model in use: +| [SPFP] - Single Precision Forces, 64-bit Fixed Point +| Accumulation. (Default) +| +|-------------------------------------------------------- + +|----------------- CITATION INFORMATION ----------------- +| +| When publishing work that utilized the CUDA version +| of AMBER, please cite the following in addition to +| the regular AMBER citations: +| +| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan +| Poole; Scott Le Grand; Ross C. Walker "Routine +| microsecond molecular dynamics simulations with +| AMBER - Part II: Particle Mesh Ewald", J. Chem. +| Theory Comput., 2013, 9 (9), pp3878-3888, +| DOI: 10.1021/ct400314y. +| +| - Andreas W. Goetz; Mark J. Williamson; Dong Xu; +| Duncan Poole; Scott Le Grand; Ross C. Walker +| "Routine microsecond molecular dynamics simulations +| with AMBER - Part I: Generalized Born", J. Chem. +| Theory Comput., 2012, 8 (5), pp1542-1555. +| +| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker +| "SPFP: Speed without compromise - a mixed precision +| model for GPU accelerated molecular dynamics +| simulations.", Comp. Phys. Comm., 2013, 184 +| pp374-380, DOI: 10.1016/j.cpc.2012.09.022 +| +| When publishing work that utilized the CUDA version +| of TI, BAR, MBAR or FEP please cite the following +| publications in addition to the regular AMBER +| GPU citations: +| +| - Daniel J. Mermelstein; Charles Lin; Gard Nelson; +| Rachael Kretsch; J. Andrew McCammon; Ross C. Walker +| "Fast and Flexible GPU Accelerated Binding +| Free Energy Calculations within the AMBER Molecular +| Dynamics Package" J. Comp. Chem., 2018, +| DOI: 10.1002/jcc.25187 +| +| - Tai-Sung Lee; Yuan Hu; Brad Sherborne; Zhuyan Guo; +| Darrin M. York +| "Toward Fast and Accurate Binding Affinity Prediction with +| pmemdGTI: An Efficient Implementation of GPU-Accelerated +| Thermodynamic Integration" +| J. Chem. Theory Comput., 2017, 13 (7), 3077 +| +| +|-------------------------------------------------------- + +|------------------- GPU DEVICE INFO -------------------- +| +| CUDA_VISIBLE_DEVICES: not set +| CUDA Capable Devices Detected: 1 +| CUDA Device ID in use: 0 +| CUDA Device Name: NVIDIA A10G +| CUDA Device Global Mem Size: 22731 MB +| CUDA Device Num Multiprocessors: 80 +| CUDA Device Core Freq: 1.71 GHz +| +|-------------------------------------------------------- + + +| Conditional Compilation Defines Used: +| PUBFFT +| BINTRAJ +| CUDA +| EMIL + +| Largest sphere to fit in unit cell has radius = 20.000 + +| New format PARM file being parsed. +| Version = 1.000 Date = 04/26/23 Time = 09:32:04 + +| Note: 1-4 EEL scale factors are being read from the topology file. + +| Note: 1-4 VDW scale factors are being read from the topology file. +| Duplicated 0 dihedrals + +| Duplicated 0 dihedrals + +-------------------------------------------------------------------------------- + 1. RESOURCE USE: +-------------------------------------------------------------------------------- + + getting new box info from bottom of inpcrd + NATOM = 6491 NTYPES = 7 NBONH = 6488 MBONA = 1 + NTHETH = 13 MTHETA = 0 NPHIH = 3 MPHIA = 0 + NHPARM = 0 NPARM = 0 NNB = 8667 NRES = 2162 + NBONA = 1 NTHETA = 0 NPHIA = 0 NUMBND = 5 + NUMANG = 3 NPTRA = 1 NATYP = 8 NPHB = 0 + IFBOX = 1 NMXRS = 6 IFCAP = 0 NEXTRA = 0 + NCOPY = 0 + +| Coordinate Index Table dimensions: 8 8 8 +| Direct force subcell size = 5.0000 5.0000 5.0000 + + BOX TYPE: RECTILINEAR + +-------------------------------------------------------------------------------- + 2. CONTROL DATA FOR THE RUN +-------------------------------------------------------------------------------- + + + +General flags: + imin = 1, nmropt = 0 + +Nature and format of input: + ntx = 1, irest = 0, ntrx = 1 + +Nature and format of output: + ntxo = 2, ntpr = 200, ntrx = 1, ntwr = 1 + iwrap = 1, ntwx = 0, ntwv = 0, ntwe = 0 + ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 + +Potential function: + ntf = 1, ntb = 1, igb = 0, nsnb = 25 + ipol = 0, gbsa = 0, iesp = 0 + dielc = 1.00000, cut = 8.00000, intdiel = 1.00000 + +Frozen or restrained atoms: + ibelly = 0, ntr = 0 + +Energy minimization: + maxcyc = 10000, ncyc = 1000, ntmin = 2 + dx0 = 0.01000, drms = 0.00010 + +Free energy options: + icfe = 1, ifsc = 1, klambda = 1 + clambda = 0.0000, scalpha = 0.5000, scbeta = 12.0000 + sceeorder = 2 + dynlmb = 0.0000 logdvdl = 0 + +| Intermolecular bonds treatment: +| no_intermolecular_bonds = 1 + +| Energy averages sample interval: +| ene_avg_sampling = 1 + +Ewald parameters: + verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1 + vdwmeth = 1, eedmeth = 1, netfrc = 0 + Box X = 40.000 Box Y = 40.000 Box Z = 40.000 + Alpha = 90.000 Beta = 90.000 Gamma = 90.000 + NFFT1 = 40 NFFT2 = 40 NFFT3 = 40 + Cutoff= 8.000 Tol =0.100E-04 + Ewald Coefficient = 0.34864 + Interpolation order = 4 + TI Mask 1 @6481-6485; matches 5 atoms + TI Mask 2 @6486-6491; matches 6 atoms + TI region 1: 6485 atoms + TI region 2: 6486 atoms + SC Mask 2 @6491; matches 1 atoms +| mismatched mass: atom #1, mass #1, atom #2, mass #26482 1.00796487 15.9994 +| gti_syn_mass has been set to 0 + +|-------------------------------------------------------------------------------------------- +| Extra TI control variables +| gti_add_sc = 1, gti_ele_gauss = 0, gti_auto_alpha = 0, gti_scale_beta = 0 +| gti_ele_exp = 2, gti_vdw_exp = 6, gti_ele_sc = 0, gti_vdw_sc = 0 +| gti_cut = 1, gti_cut_sc = 0 +| gti_cut_sc_on = 0.0000, gti_cut_sc_off = 0.0000 +|-------------------------------------------------------------------------------------------- + + +-------------------------------------------------------------------------------- + 3. ATOMIC COORDINATES AND VELOCITIES +-------------------------------------------------------------------------------- + + + begin time read from input coords = 0.000 ps + + + Number of triangulated 3-point waters found: 2160 + Number of shake restraints removed in TI region 1 : 0 + Number of shake restraints removed in TI region 2 : 0 + + Sum of charges for TI region 1 = -0.00000000 + Skip neutralizing charges... + + + Sum of charges for TI region 2 = -0.00000000 + Skip neutralizing charges... + +| Dynamic Memory, Types Used: +| Reals 343770 +| Integers 277189 + +| Nonbonded Pairs Initial Allocation: 1084159 + +| GPU memory information (estimate): +| KB of GPU memory in use: 24829 +| KB of CPU memory in use: 14077 + +-------------------------------------------------------------------------------- + 4. RESULTS +-------------------------------------------------------------------------------- + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1 1.1499E+04 1.3559E+02 3.3411E+03 O 4411 + + BOND = 21543.4552 ANGLE = 3.3520 DIHED = 0.0000 + VDWAALS = 14714.9925 EEL = -24763.0744 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.5181 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1 1.1499E+04 1.3559E+02 3.3411E+03 O 4411 + + BOND = 21543.4552 ANGLE = 3.3520 DIHED = 0.0000 + VDWAALS = 14714.9925 EEL = -24763.0744 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.5181 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 7.9803 + SC_BOND= 6.0790 SC_ANGLE= 1.9012 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 200 -2.5313E+04 7.4760E-01 4.8672E+00 H2 540 + + BOND = 1704.8992 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 3760.4348 EEL = -30781.6359 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1081 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 200 -2.5313E+04 7.4760E-01 4.8672E+00 H2 540 + + BOND = 1704.8992 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 3760.4348 EEL = -30781.6359 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1081 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0004 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0004 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 400 -2.5996E+04 4.0016E-01 3.2874E+00 H1 1691 + + BOND = 1824.6795 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 4020.7338 EEL = -31845.2484 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3625 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 400 -2.5996E+04 4.0016E-01 3.2874E+00 H1 1691 + + BOND = 1824.6795 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 4020.7338 EEL = -31845.2484 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3625 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0002 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0002 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 600 -2.6340E+04 3.0200E-01 3.1083E+00 H1 6098 + + BOND = 1891.7485 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4243.2699 EEL = -32478.7110 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.4309 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 600 -2.6340E+04 3.0200E-01 3.1083E+00 H1 6098 + + BOND = 1891.7485 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4243.2699 EEL = -32478.7110 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.4309 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 800 -2.6554E+04 1.0464E+00 5.1517E+00 H2 1476 + + BOND = 2010.3193 ANGLE = 3.3521 DIHED = 0.0000 + VDWAALS = 4400.9632 EEL = -32968.7103 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.4135 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 800 -2.6554E+04 1.0464E+00 5.1517E+00 H2 1476 + + BOND = 2010.3193 ANGLE = 3.3521 DIHED = 0.0000 + VDWAALS = 4400.9632 EEL = -32968.7103 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.4135 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1000 -2.6715E+04 2.2513E-01 2.1955E+00 H1 4319 + + BOND = 1970.1512 ANGLE = 3.3521 DIHED = 0.0000 + VDWAALS = 4521.0533 EEL = -33209.6105 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3816 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1000 -2.6715E+04 2.2513E-01 2.1955E+00 H1 4319 + + BOND = 1970.1512 ANGLE = 3.3521 DIHED = 0.0000 + VDWAALS = 4521.0533 EEL = -33209.6105 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3816 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1200 -2.6835E+04 5.8174E-01 2.8164E+00 H1 4166 + + BOND = 2038.3518 ANGLE = 3.3521 DIHED = 0.0000 + VDWAALS = 4617.6099 EEL = -33494.8132 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3747 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1200 -2.6835E+04 5.8174E-01 2.8164E+00 H1 4166 + + BOND = 2038.3518 ANGLE = 3.3521 DIHED = 0.0000 + VDWAALS = 4617.6099 EEL = -33494.8132 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3747 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1400 -2.6936E+04 2.3301E-01 2.0474E+00 H2 3969 + + BOND = 2032.9094 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4697.3766 EEL = -33669.5917 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3875 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1400 -2.6936E+04 2.3301E-01 2.0474E+00 H2 3969 + + BOND = 2032.9094 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4697.3766 EEL = -33669.5917 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3875 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1600 -2.7019E+04 1.6148E-01 1.6976E+00 H2 4251 + + BOND = 2043.4513 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4771.5801 EEL = -33837.4569 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3980 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1600 -2.7019E+04 1.6148E-01 1.6976E+00 H2 4251 + + BOND = 2043.4513 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4771.5801 EEL = -33837.4569 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3980 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1800 -2.7089E+04 1.6200E-01 2.3338E+00 H2 2775 + + BOND = 2060.9356 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4838.2339 EEL = -33992.0185 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3987 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 1800 -2.7089E+04 1.6200E-01 2.3338E+00 H2 2775 + + BOND = 2060.9356 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4838.2339 EEL = -33992.0185 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3987 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2000 -2.7149E+04 4.1294E-01 2.1239E+00 H2 3417 + + BOND = 2045.0517 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4898.7041 EEL = -34096.6041 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3837 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2000 -2.7149E+04 4.1294E-01 2.1239E+00 H2 3417 + + BOND = 2045.0517 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4898.7041 EEL = -34096.6041 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3837 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2200 -2.7200E+04 1.6472E-01 1.4876E+00 H1 2936 + + BOND = 2075.3102 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4947.6372 EEL = -34226.4572 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3495 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2200 -2.7200E+04 1.6472E-01 1.4876E+00 H1 2936 + + BOND = 2075.3102 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4947.6372 EEL = -34226.4572 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3495 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2400 -2.7247E+04 1.5303E-01 2.1312E+00 H1 2936 + + BOND = 2086.6480 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4989.7635 EEL = -34326.3429 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3221 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2400 -2.7247E+04 1.5303E-01 2.1312E+00 H1 2936 + + BOND = 2086.6480 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 4989.7635 EEL = -34326.3429 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3221 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2600 -2.7289E+04 4.3080E-01 2.3542E+00 H2 3417 + + BOND = 2130.7597 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5029.8658 EEL = -34452.8365 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3194 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2600 -2.7289E+04 4.3080E-01 2.3542E+00 H2 3417 + + BOND = 2130.7597 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5029.8658 EEL = -34452.8365 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3194 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2800 -2.7325E+04 1.8008E-01 1.3887E+00 H2 1929 + + BOND = 2121.1833 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5067.2455 EEL = -34516.5502 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3215 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 2800 -2.7325E+04 1.8008E-01 1.3887E+00 H2 1929 + + BOND = 2121.1833 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5067.2455 EEL = -34516.5502 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3215 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3000 -2.7356E+04 1.0391E-01 1.5075E+00 H2 1929 + + BOND = 2121.2322 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5100.8429 EEL = -34581.5094 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3315 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3000 -2.7356E+04 1.0391E-01 1.5075E+00 H2 1929 + + BOND = 2121.2322 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5100.8429 EEL = -34581.5094 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3315 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3200 -2.7386E+04 1.0960E-01 1.8598E+00 H2 3018 + + BOND = 2129.4279 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5131.7968 EEL = -34650.4821 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3688 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3200 -2.7386E+04 1.0960E-01 1.8598E+00 H2 3018 + + BOND = 2129.4279 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5131.7968 EEL = -34650.4821 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3688 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3400 -2.7417E+04 2.6815E-01 2.3406E+00 H2 6192 + + BOND = 2116.6091 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5159.9546 EEL = -34697.1378 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.4091 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3400 -2.7417E+04 2.6815E-01 2.3406E+00 H2 6192 + + BOND = 2116.6091 ANGLE = 3.3522 DIHED = 0.0000 + VDWAALS = 5159.9546 EEL = -34697.1378 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.4091 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3600 -2.7449E+04 1.6588E-01 2.7897E+00 H1 1433 + + BOND = 2130.5995 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 5186.4139 EEL = -34769.2096 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3908 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3600 -2.7449E+04 1.6588E-01 2.7897E+00 H1 1433 + + BOND = 2130.5995 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 5186.4139 EEL = -34769.2096 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3908 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3800 -2.7476E+04 1.0466E-01 1.2861E+00 H1 6191 + + BOND = 2141.8324 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 5211.1123 EEL = -34832.4374 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3635 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 3800 -2.7476E+04 1.0466E-01 1.2861E+00 H1 6191 + + BOND = 2141.8324 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 5211.1123 EEL = -34832.4374 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3635 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4000 -2.7499E+04 2.8003E-01 1.6410E+00 H2 3417 + + BOND = 2168.8902 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 5231.0318 EEL = -34902.1200 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3344 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4000 -2.7499E+04 2.8003E-01 1.6410E+00 H2 3417 + + BOND = 2168.8902 ANGLE = 3.3523 DIHED = 0.0000 + VDWAALS = 5231.0318 EEL = -34902.1200 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3344 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4200 -2.7521E+04 1.8689E-01 2.0019E+00 H2 318 + + BOND = 2166.4459 ANGLE = 3.3524 DIHED = 0.0000 + VDWAALS = 5247.5300 EEL = -34938.1821 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3046 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4200 -2.7521E+04 1.8689E-01 2.0019E+00 H2 318 + + BOND = 2166.4459 ANGLE = 3.3524 DIHED = 0.0000 + VDWAALS = 5247.5300 EEL = -34938.1821 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.3046 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4400 -2.7542E+04 8.3454E-02 1.9473E+00 H1 3059 + + BOND = 2160.8042 ANGLE = 3.3524 DIHED = 0.0000 + VDWAALS = 5263.3079 EEL = -34969.3209 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.2720 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4400 -2.7542E+04 8.3454E-02 1.9473E+00 H1 3059 + + BOND = 2160.8042 ANGLE = 3.3524 DIHED = 0.0000 + VDWAALS = 5263.3079 EEL = -34969.3209 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.2720 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4600 -2.7560E+04 2.4918E-01 1.5941E+00 H1 3059 + + BOND = 2147.2125 ANGLE = 3.3524 DIHED = 0.0000 + VDWAALS = 5279.1747 EEL = -34990.0673 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.2387 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4600 -2.7560E+04 2.4918E-01 1.5941E+00 H1 3059 + + BOND = 2147.2125 ANGLE = 3.3524 DIHED = 0.0000 + VDWAALS = 5279.1747 EEL = -34990.0673 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.2387 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4800 -2.7578E+04 1.0279E-01 1.6598E+00 H2 6405 + + BOND = 2161.9475 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5294.1524 EEL = -35037.1418 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.2069 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 4800 -2.7578E+04 1.0279E-01 1.6598E+00 H2 6405 + + BOND = 2161.9475 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5294.1524 EEL = -35037.1418 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.2069 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5000 -2.7596E+04 3.2144E-01 2.0369E+00 H1 6404 + + BOND = 2191.7135 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5309.5135 EEL = -35100.2438 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1775 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5000 -2.7596E+04 3.2144E-01 2.0369E+00 H1 6404 + + BOND = 2191.7135 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5309.5135 EEL = -35100.2438 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1775 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5200 -2.7615E+04 2.3273E-01 1.7487E+00 H1 50 + + BOND = 2189.1502 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5324.9049 EEL = -35132.5404 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1497 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5200 -2.7615E+04 2.3273E-01 1.7487E+00 H1 50 + + BOND = 2189.1502 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5324.9049 EEL = -35132.5404 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1497 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5400 -2.7634E+04 1.0396E-01 1.5977E+00 H1 4895 + + BOND = 2182.7028 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5340.1326 EEL = -35160.0420 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1214 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5400 -2.7634E+04 1.0396E-01 1.5977E+00 H1 4895 + + BOND = 2182.7028 ANGLE = 3.3525 DIHED = 0.0000 + VDWAALS = 5340.1326 EEL = -35160.0420 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.1214 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5600 -2.7651E+04 3.1411E-01 1.7089E+00 H1 4832 + + BOND = 2161.1523 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5354.7197 EEL = -35170.5622 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.0928 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5600 -2.7651E+04 3.1411E-01 1.7089E+00 H1 4832 + + BOND = 2161.1523 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5354.7197 EEL = -35170.5622 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.0928 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5800 -2.7666E+04 2.2644E-01 1.2263E+00 H1 4832 + + BOND = 2170.4279 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5369.4205 EEL = -35208.8913 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.0582 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 5800 -2.7666E+04 2.2644E-01 1.2263E+00 H1 4832 + + BOND = 2170.4279 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5369.4205 EEL = -35208.8913 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.0582 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6000 -2.7678E+04 1.6714E-01 9.6218E-01 H2 3003 + + BOND = 2177.5210 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5381.1876 EEL = -35240.3918 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.0267 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6000 -2.7678E+04 1.6714E-01 9.6218E-01 H2 3003 + + BOND = 2177.5210 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5381.1876 EEL = -35240.3918 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 39.0267 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6200 -2.7690E+04 6.4074E-02 9.6690E-01 O 3940 + + BOND = 2189.2849 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5389.9157 EEL = -35272.7892 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9981 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6200 -2.7690E+04 6.4074E-02 9.6690E-01 O 3940 + + BOND = 2189.2849 ANGLE = 3.3526 DIHED = 0.0000 + VDWAALS = 5389.9157 EEL = -35272.7892 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9981 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6400 -2.7702E+04 2.2123E-01 1.3664E+00 H1 4832 + + BOND = 2207.2116 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5396.5875 EEL = -35308.9058 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9712 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6400 -2.7702E+04 2.2123E-01 1.3664E+00 H1 4832 + + BOND = 2207.2116 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5396.5875 EEL = -35308.9058 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9712 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6600 -2.7713E+04 1.6008E-01 1.2019E+00 H1 2558 + + BOND = 2204.7385 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5401.8316 EEL = -35323.1978 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9477 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6600 -2.7713E+04 1.6008E-01 1.2019E+00 H1 2558 + + BOND = 2204.7385 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5401.8316 EEL = -35323.1978 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9477 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6800 -2.7724E+04 5.9749E-02 8.4824E-01 H2 3363 + + BOND = 2197.5682 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5407.0909 EEL = -35331.7572 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9336 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 6800 -2.7724E+04 5.9749E-02 8.4824E-01 H2 3363 + + BOND = 2197.5682 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5407.0909 EEL = -35331.7572 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9336 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7000 -2.7734E+04 6.3562E-02 1.1188E+00 H1 6407 + + BOND = 2200.1967 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5412.2633 EEL = -35349.4606 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9218 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7000 -2.7734E+04 6.3562E-02 1.1188E+00 H1 6407 + + BOND = 2200.1967 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5412.2633 EEL = -35349.4606 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9218 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7200 -2.7743E+04 9.4737E-02 1.4149E+00 H1 6407 + + BOND = 2194.8038 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5416.9807 EEL = -35358.5061 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9115 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7200 -2.7743E+04 9.4737E-02 1.4149E+00 H1 6407 + + BOND = 2194.8038 ANGLE = 3.3527 DIHED = 0.0000 + VDWAALS = 5416.9807 EEL = -35358.5061 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9115 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7400 -2.7753E+04 5.9339E-02 1.4802E+00 H2 4896 + + BOND = 2200.3428 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5421.1203 EEL = -35377.8461 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9045 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7400 -2.7753E+04 5.9339E-02 1.4802E+00 H2 4896 + + BOND = 2200.3428 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5421.1203 EEL = -35377.8461 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.9045 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7600 -2.7763E+04 1.9516E-01 1.3038E+00 H1 5468 + + BOND = 2215.7730 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5425.1380 EEL = -35407.1269 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8971 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7600 -2.7763E+04 1.9516E-01 1.3038E+00 H1 5468 + + BOND = 2215.7730 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5425.1380 EEL = -35407.1269 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8971 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0000 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7800 -2.7773E+04 1.4791E-01 1.1135E+00 H1 1325 + + BOND = 2214.0738 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5430.2064 EEL = -35420.4469 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8876 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 7800 -2.7773E+04 1.4791E-01 1.1135E+00 H1 1325 + + BOND = 2214.0738 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5430.2064 EEL = -35420.4469 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8876 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8000 -2.7783E+04 8.0831E-02 1.7602E+00 H1 1325 + + BOND = 2210.1686 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5434.8996 EEL = -35431.5782 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8782 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8000 -2.7783E+04 8.0831E-02 1.7602E+00 H1 1325 + + BOND = 2210.1686 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5434.8996 EEL = -35431.5782 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8782 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8200 -2.7794E+04 1.9268E-01 1.3871E+00 H1 5417 + + BOND = 2196.0768 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5438.9671 EEL = -35432.7749 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8688 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8200 -2.7794E+04 1.9268E-01 1.3871E+00 H1 5417 + + BOND = 2196.0768 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5438.9671 EEL = -35432.7749 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8688 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8400 -2.7806E+04 7.8410E-02 2.1105E+00 H1 1766 + + BOND = 2206.6145 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5444.5118 EEL = -35460.3037 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8566 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8400 -2.7806E+04 7.8410E-02 2.1105E+00 H1 1766 + + BOND = 2206.6145 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5444.5118 EEL = -35460.3037 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8566 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8600 -2.7817E+04 6.0181E-02 1.9512E+00 H1 1766 + + BOND = 2210.4329 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5450.8601 EEL = -35481.4094 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8474 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8600 -2.7817E+04 6.0181E-02 1.9512E+00 H1 1766 + + BOND = 2210.4329 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5450.8601 EEL = -35481.4094 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8474 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8800 -2.7826E+04 1.8474E-01 1.4074E+00 H1 5468 + + BOND = 2225.1613 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5457.2249 EEL = -35511.5731 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8445 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 8800 -2.7826E+04 1.8474E-01 1.4074E+00 H1 5468 + + BOND = 2225.1613 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5457.2249 EEL = -35511.5731 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8445 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9000 -2.7834E+04 1.3825E-01 1.4699E+00 H2 5439 + + BOND = 2223.3723 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5462.8680 EEL = -35524.0781 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8425 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9000 -2.7834E+04 1.3825E-01 1.4699E+00 H2 5439 + + BOND = 2223.3723 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5462.8680 EEL = -35524.0781 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8425 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9200 -2.7843E+04 2.4457E-01 1.9140E+00 H2 5550 + + BOND = 2200.5830 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5469.1132 EEL = -35515.6408 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8386 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9200 -2.7843E+04 2.4457E-01 1.9140E+00 H2 5550 + + BOND = 2200.5830 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5469.1132 EEL = -35515.6408 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8386 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9400 -2.7850E+04 5.4301E-02 1.5701E+00 H2 2064 + + BOND = 2219.5546 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5475.8111 EEL = -35549.0738 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8215 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9400 -2.7850E+04 5.4301E-02 1.5701E+00 H2 2064 + + BOND = 2219.5546 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5475.8111 EEL = -35549.0738 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8215 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9600 -2.7857E+04 1.3261E-01 2.6548E+00 H2 2064 + + BOND = 2211.2580 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5483.0506 EEL = -35554.9611 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.7792 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9600 -2.7857E+04 1.3261E-01 2.6548E+00 H2 2064 + + BOND = 2211.2580 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5483.0506 EEL = -35554.9611 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.7792 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9800 -2.7863E+04 9.8227E-02 8.3969E-01 H2 2064 + + BOND = 2214.8176 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5489.4566 EEL = -35570.9401 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.7747 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 9800 -2.7863E+04 9.8227E-02 8.3969E-01 H2 2064 + + BOND = 2214.8176 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5489.4566 EEL = -35570.9401 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.7747 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 10000 -2.7868E+04 1.7519E-01 1.4445E+00 H2 5550 + + BOND = 2233.0302 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5493.6372 EEL = -35598.0883 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8001 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 10000 -2.7868E+04 1.7519E-01 1.4445E+00 H2 5550 + + BOND = 2233.0302 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5493.6372 EEL = -35598.0883 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8001 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + + + + Maximum number of minimization cycles reached. + + + FINAL RESULTS + + +| TI region 1 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 10000 -2.7868E+04 1.7519E-01 1.4445E+00 H2 5550 + + BOND = 2233.0302 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5493.6372 EEL = -35598.0883 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8001 + +| TI region 2 + + + + NSTEP ENERGY RMS GMAX NAME NUMBER + 10000 -2.7868E+04 1.7519E-01 1.4445E+00 H2 5550 + + BOND = 2233.0302 ANGLE = 3.3528 DIHED = 0.0000 + VDWAALS = 5493.6372 EEL = -35598.0883 HBOND = 0.0000 + 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT = 0.0000 + DV/DL = 38.8001 + Softcore part of the system: 1 atoms, TEMP(K) = 0.00 + SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot = 0.0001 + SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0001 + SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000 + SC_EEL = 0.0000 + SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000 + SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000 + ------------------------------------------------------------------------------ + +-------------------------------------------------------------------------------- + 5. TIMINGS +-------------------------------------------------------------------------------- + +| NonSetup CPU Time in Major Routines: +| +| Routine Sec % +| ------------------------------ +| Nonbond 2.79 51.61 +| Bond 0.00 0.00 +| Angle 0.00 0.00 +| Dihedral 0.00 0.00 +| Shake 0.00 0.00 +| Other 2.62 48.39 +| ------------------------------ +| Total 5.41 + +| PME Nonbond Pairlist CPU Time: +| +| Routine Sec % +| --------------------------------- +| Set Up Cit 0.00 0.00 +| Build List 0.00 0.00 +| --------------------------------- +| Total 0.00 0.00 + +| PME Direct Force CPU Time: +| +| Routine Sec % +| --------------------------------- +| NonBonded Calc 0.00 0.00 +| Exclude Masked 0.00 0.00 +| Other 0.01 0.21 +| --------------------------------- +| Total 0.01 0.21 + +| PME Reciprocal Force CPU Time: +| +| Routine Sec % +| --------------------------------- +| 1D bspline 0.00 0.00 +| Grid Charges 0.00 0.00 +| Scalar Sum 0.00 0.00 +| Gradient Sum 0.00 0.00 +| FFT 0.00 0.00 +| --------------------------------- +| Total 0.00 0.00 + +| Setup CPU time: 0.23 seconds +| NonSetup CPU time: 5.41 seconds +| Total CPU time: 5.64 seconds 0.00 hours + +| Setup wall time: 7 seconds +| NonSetup wall time: 11 seconds +| Total wall time: 18 seconds 0.01 hours