From 9c82b28323956eb115f8bc7591699ca961a024fc Mon Sep 17 00:00:00 2001 From: Alec <30010253+alec-glisman@users.noreply.github.com> Date: Mon, 15 Apr 2024 12:02:38 -0700 Subject: [PATCH] added 1000 ns run files and corrected NPT eqbm time --- .../mdp/molecular-dynamics/npt_eqbm.mdp | 2 +- .../molecular-dynamics/npt_prod_1000ns.mdp | 61 +++++++++++++++++++ .../molecular-dynamics/nvt_prod_1000ns.mdp | 60 ++++++++++++++++++ scripts/method/equilibration.sh | 6 +- ...A_0Ca_104calcite_2nm_crystal_5nm_height.sh | 2 +- ...A_0Ca_104calcite_5nm_crystal_6nm_height.sh | 2 +- ...2Ca_104calcite_12nm_crystal_12nm_height.sh | 2 +- ...A_0Ca_104calcite_2nm_crystal_3nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_3nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_4nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_3nm_height.sh | 2 +- ...A_0Ca_104calcite_1nm_crystal_4nm_height.sh | 2 +- ...A_0Ca_104calcite_2nm_crystal_4nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ..._0Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...A_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ...n_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ...c_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ...H_0Ca_104calcite_5nm_crystal_8nm_height.sh | 2 +- ..._8Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...32Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...64Ca_104calcite_9nm_crystal_10nm_height.sh | 2 +- .../1.0_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...aCl2_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...aCO3_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16AA_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16An_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16Al_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16Ac_104calcite_9nm_crystal_10nm_height.sh | 2 +- .../5-one-opes-params/1.0_lowbarrier3.sh | 2 +- .../5-one-opes-params/2.0_lowbarrier5.sh | 2 +- .../3.0_lowbarrier5_geom370.sh | 2 +- .../4.0_lowbarrier5_geom350.sh | 2 +- .../5.0_lowbarrier5_lower305_geom370.sh | 2 +- .../6.0_lowbarrier5_lower304_upper374.sh | 2 +- .../7.0_lowbarrier8_lower304_upper374.sh | 2 +- .../1.0_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.1_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.2_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.3_16paa_0Ca_9nmcrystal.sh | 2 +- .../1.4_16paa_0Ca_9nmcrystal.sh | 2 +- .../2.0_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.1_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.2_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.3_16paan_0Ca_9nmcrystal.sh | 2 +- .../2.4_16paan_0Ca_9nmcrystal.sh | 2 +- .../3.0_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.1_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.2_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.3_32paa_0Ca_12nmcrystal.sh | 2 +- .../3.4_32paa_0Ca_12nmcrystal.sh | 2 +- .../4.0_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.1_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.2_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.3_32paan_0Ca_12nmcrystal.sh | 2 +- .../4.4_32paan_0Ca_12nmcrystal.sh | 2 +- .../5.0_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.1_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.2_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.3_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../5.4_32paa_32CaCl2_12nmcrystal.sh | 2 +- .../1.0_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...aCl2_104calcite_9nm_crystal_10nm_height.sh | 2 +- ...16AA_104calcite_9nm_crystal_10nm_height.sh | 2 +- .../4.0_16paa_0Ca_9nmcrystal.sh | 2 +- 72 files changed, 193 insertions(+), 72 deletions(-) create mode 100644 parameters/mdp/molecular-dynamics/npt_prod_1000ns.mdp create mode 100644 parameters/mdp/molecular-dynamics/nvt_prod_1000ns.mdp diff --git a/parameters/mdp/molecular-dynamics/npt_eqbm.mdp b/parameters/mdp/molecular-dynamics/npt_eqbm.mdp index f57d190..8871727 100644 --- a/parameters/mdp/molecular-dynamics/npt_eqbm.mdp +++ b/parameters/mdp/molecular-dynamics/npt_eqbm.mdp @@ -5,7 +5,7 @@ ;;; Run control ;;; integrator = md ; "steep" for energy minimization and "md" for a leap frog algorithm for integrating Newton's eq of motion dt = 0.001 ; 1 femtosecond -nsteps = 500000 ; 1 nanosecond +nsteps = 5000000 ; 5 nanoseconds comm-mode = Linear ; "Linear" (remove center for mass translation) "Angular" ( >> >> and rotation around the center of mass) "None" (no restric) nstcomm = 100 ; [steps] frequency for center of mass motion removal comm-grps = Aqueous Crystal ; groups for which the center of mass motion is removed diff --git a/parameters/mdp/molecular-dynamics/npt_prod_1000ns.mdp b/parameters/mdp/molecular-dynamics/npt_prod_1000ns.mdp new file mode 100644 index 0000000..1bc5d67 --- /dev/null +++ b/parameters/mdp/molecular-dynamics/npt_prod_1000ns.mdp @@ -0,0 +1,61 @@ +; Created by Alec Glisman (GitHub: @alec-glisman) on December 31st, 2021 +;;; GROMACS Documentation: https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html ;;; +;;; Defines ;;; +; define = -DPOSRES_CRYSTAL ; defines a macro that can be used in the topology file +;;; Run control ;;; +integrator = md ; "steep" for ener minimization and "md" for a leap frog algorithm for integrating Newton's eq of motion +dt = 0.002 ; 2 femtoseconds +nsteps = 500000000 ; 1000 nanoseconds +comm-mode = Linear ; "Linear" (remove center for mass translation) "Angular" ( >> >> and rotation around the center of mass) "None" (no restric) +nstcomm = 100 ; [steps] frequency for center of mass motion removal +comm-grps = Aqueous Crystal ; groups for which the center of mass motion is removed +;;; Output control ;;; +nstxout = 0 ; [steps] number of steps that elapse between writing coordinates to the output trajectory file (trr) +nstvout = 0 ; [steps] number of steps that elapse between writing velocities to the output trajectory file (trr) +nstfout = 0 ; [steps] number of steps that elapse between writing forces to the output trajectory file (trr) +nstcalcenergy = 100 ; [steps] number of steps that elapse between calculating the energies, 0 is never +nstenergy = 1000 ; [steps] number of steps that elapse between writing energies to energy file +nstlog = 1000 ; [steps] number of steps that elapse between writing energies to the log file +nstxout-compressed = 1000 ; [steps] number of steps that elapse between writing to .xtc file +;;; Neighbor searching ;;; +cutoff-scheme = Verlet ; algorithm to generate neigbor list +nstlist = 10 ; [steps] frequency to update the neighbor list +pbc = xyz ; periodic boundary conditions +rlist = 1.2000 ; [nm] cut-off distance for the short-range neighbor list +;;; Electrostatics ;;; +coulombtype = PME ; algorithm to generate electrostatics +rcoulomb = 1.2000 ; [nm] The distance for the Coulomb cut-off +;;; Van der Waals ;;; +vdw-type = cut-off ; algorithm to generate Van der Waals +rvdw = 1.2000 ; [nm] distance for the LJ or Buckingham cut-off +DispCorr = AllEnerPres ; corrections to apply for long-ranged energy and/or pressure +;;; Ewald ;;; +fourierspacing = 0.12 ; [nm] for ordinary Ewald, the ratio of the box dimensions and the spacing determines a lower bound for the number of wave vectors to use in each (signed) direction +pme-order = 4 ; interpolation order for PME. 4 equals cubic interpolation. +ewald-rtol = 1.0e-5 ; the relative strength of the Ewald-shifted direct potential at rcoulomb +ewald-geometry = 3d ; "3d" is the ewald sum which is performed in all the three dimensions or "3dc" the reciprocal sum is still performed in 3D but a forec and potential correction applied in the z dimension to produce a pseudo 2D summation +;;; Temperature coupling ;;; +Tcoupl = nose-hoover ; Temp coupling using velocity rescaling. Temperature coupling using a Nose-Hoover extended ensemble. The reference temperature and coupling groups are selected as above, but in this case tau-t controls the period of the temperature fluctuations at equilibrium, which is slightly different from a relaxation time. For NVT simulations the conserved energy quantity is written to the energy and log files. +tc-grps = System ; groups to couple separately to Temp bath +tau-t = 0.50 ; [ps] time constant for coupling (one for each group in tc-grps) +ref-t = 300 ; [K] reference temperature for coupling (one for each group in tc-grps) +;;; Pressure Coupling ;;; +Pcoupl = Parrinello-Rahman ; No pressure coupling, This means fixed box size. Extended-ensemble pressure coupling where the box vectors are subject to an equation of motion. The equation of motion for the atoms is coupled to this. No instantaneous scaling takes place. +Pcoupltype = semiisotropic ; specifies the kind of isotropy of the pressure coupling used. +tau-p = 5.0 ; [ps] The time constant for pressure coupling (one value for all directions). +ref-p = 1.0 1.0 ; [bar] the reference pressure for coupling +compressibility = 4.5e-15 4.5e-5 ; [bar^{-1}] for water at 1 atm and 300K the compressibility is 4.5e-5 bar-1 +;;; Velocity generation ;;; +gen-vel = no ; "no" do not generate velocities "yes" generate velocities in grompp at temp gen-temp which is only meanigful with integrator "md" +gen-temp = 300 ; [K] temperature for Maxwell distribution +;;; Bonds ;;; +constraints = h-bonds ; controls which bonds in the topology will be converted to rigid holonomic constraints. +constraint-algorithm = lincs ; chooses which solver satisfies any non-SETTLE holonomic constraints. "lincs" is faster but does not work with angle constraints +lincs-order = 4 ; accuracy of lincs: the number of matrices in the expansion for the matrix inversion +lincs-iter = 1 ; number of iterative corrections to matrix inversion to compensate for lengthening due to rotation +lincs-warnangle = 30 ; print warning to log file and stderr if bond rotations be more than this angle +;;; Vacuum parameters ;;; +nwall = 0 ; number of walls +wall-type = 9-3 ; type of wall potential +wall-atomtype = WR WL ; the atom type name in the force field for each wall. +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/parameters/mdp/molecular-dynamics/nvt_prod_1000ns.mdp b/parameters/mdp/molecular-dynamics/nvt_prod_1000ns.mdp new file mode 100644 index 0000000..63a78b6 --- /dev/null +++ b/parameters/mdp/molecular-dynamics/nvt_prod_1000ns.mdp @@ -0,0 +1,60 @@ +; Created by Alec Glisman (GitHub: @alec-glisman) on December 31st, 2021 +;;; GROMACS Documentation: https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html ;;; +;;; Defines ;;; +; define = -DPOSRES_CRYSTAL ; defines a macro that can be used in the topology file +;;; Run control ;;; +integrator = md ; "steep" for ener minimization and "md" for a leap frog algorithm for integrating Newton's eq of motion +dt = 0.002 ; 2 femtoseconds +nsteps = 500000000 ; 1000 nanoseconds +comm-mode = Linear ; "Linear" (remove center for mass translation) "Angular" ( >> >> and rotation around the center of mass) "None" (no restric) +nstcomm = 100 ; [steps] frequency for center of mass motion removal +comm-grps = Aqueous Crystal ; groups for which the center of mass motion is removed +;;; Output control ;;; +nstxout = 0 ; [steps] number of steps that elapse between writing coordinates to the output trajectory file (trr) +nstvout = 0 ; [steps] number of steps that elapse between writing velocities to the output trajectory file (trr) +nstfout = 0 ; [steps] number of steps that elapse between writing forces to the output trajectory file (trr) +nstcalcenergy = 100 ; [steps] number of steps that elapse between calculating the energies, 0 is never +nstenergy = 1000 ; [steps] number of steps that elapse between writing energies to energy file +nstlog = 1000 ; [steps] number of steps that elapse between writing energies to the log file +nstxout-compressed = 1000 ; [steps] number of steps that elapse between writing to .xtc file +;;; Neighbor searching ;;; +cutoff-scheme = Verlet ; algorithm to generate neigbor list +nstlist = 10 ; [steps] frequency to update the neighbor list +pbc = xyz ; periodic boundary conditions +rlist = 1.2000 ; [nm] cut-off distance for the short-range neighbor list +;;; Electrostatics ;;; +coulombtype = PME ; algorithm to generate electrostatics +rcoulomb = 1.2000 ; [nm] The distance for the Coulomb cut-off +;;; Van der Waals ;;; +vdw-type = cut-off ; algorithm to generate Van der Waals +rvdw = 1.2000 ; [nm] distance for the LJ or Buckingham cut-off +DispCorr = AllEnerPres ; corrections to apply for long-ranged energy and/or pressure +;;; Ewald ;;; +fourierspacing = 0.12 ; [nm] for ordinary Ewald, the ratio of the box dimensions and the spacing determines a lower bound for the number of wave vectors to use in each (signed) direction +pme-order = 4 ; interpolation order for PME. 4 equals cubic interpolation. +ewald-rtol = 1.0e-5 ; the relative strength of the Ewald-shifted direct potential at rcoulomb +ewald-geometry = 3d ; "3d" is the ewald sum which is performed in all the three dimensions or "3dc" the reciprocal sum is still performed in 3D but a forec and potential correction applied in the z dimension to produce a pseudo 2D summation +;;; Temperature coupling ;;; +Tcoupl = nose-hoover ; Temp coupling using velocity rescaling. Temperature coupling using a Nose-Hoover extended ensemble. The reference temperature and coupling groups are selected as above, but in this case tau-t controls the period of the temperature fluctuations at equilibrium, which is slightly different from a relaxation time. For NVT simulations the conserved energy quantity is written to the energy and log files. +tc-grps = System ; groups to couple separately to Temp bath +tau-t = 0.50 ; [ps] time constant for coupling (one for each group in tc-grps) +ref-t = 300 ; [K] reference temperature for coupling (one for each group in tc-grps) +;;; Pressure Coupling ;;; +Pcoupl = no ; no pressure coupling in NVT +;;; Velocity generation ;;; +gen-vel = no ; "no" do not generate velocities "yes" generate velocities in grompp at temp gen-temp which is only meanigful with integrator "md" +gen-temp = 300 ; [K] temperature for Maxwell distribution +;;; Bonds ;;; +constraints = h-bonds ; controls which bonds in the topology will be converted to rigid holonomic constraints. +constraint-algorithm = lincs ; chooses which solver satisfies any non-SETTLE holonomic constraints. "lincs" is faster but does not work with angle constraints +lincs-order = 4 ; accuracy of lincs: the number of matrices in the expansion for the matrix inversion +lincs-iter = 1 ; number of iterative corrections to matrix inversion to compensate for lengthening due to rotation +lincs-warnangle = 30 ; print warning to log file and stderr if bond rotations be more than this angle +;;; Frozen groups ;;; +freezegrps = Frozen ; groups that are to be frozen +freezedim = Y Y Y ; directions in which the groups are frozen +;;; Vacuum parameters ;;; +nwall = 0 ; number of walls +wall-type = 9-3 ; type of wall potential +wall-atomtype = WR WL ; the atom type name in the force field for each wall. +wall-density = 50 50 ; [nm-3] / [nm-2] the number density of the atoms for each wall diff --git a/scripts/method/equilibration.sh b/scripts/method/equilibration.sh index 3cbc014..e19342f 100755 --- a/scripts/method/equilibration.sh +++ b/scripts/method/equilibration.sh @@ -216,9 +216,6 @@ else -o "${sim_name}.tpr" rm "${previous_sim_name}.gro" || exit 1 - # plumed performance - export PLUMED_NUM_THREADS="${CPU_THREADS}" - # run NPT equilibration # shellcheck disable=SC2086 "${GMX_BIN}" -nocopyright mdrun -v \ @@ -388,6 +385,9 @@ else sed -i 's/#RESTART/RESTART/g' "plumed.dat" || exit 1 fi + # plumed performance + export PLUMED_NUM_THREADS="${CPU_THREADS}" + # run production equilibration # shellcheck disable=SC2086 "${GMX_BIN}" -nocopyright mdrun -v \ diff --git a/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh b/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh index 3aa6054..e6face0 100755 --- a/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh +++ b/submission/input/0-goddard-tests/1.0_1PAA_0Ca_104calcite_2nm_crystal_5nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh b/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh index 7954ff8..882984e 100755 --- a/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh +++ b/submission/input/0-goddard-tests/2.0_8PAA_0Ca_104calcite_5nm_crystal_6nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh b/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh index db8a880..4e16ae4 100755 --- a/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh +++ b/submission/input/0-goddard-tests/3.0_32PAA_32Ca_104calcite_12nm_crystal_12nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh index 5afbcc6..7b42545 100755 --- a/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/4.0_3PAA_0Ca_104calcite_2nm_crystal_3nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh index 37f074a..0279056 100755 --- a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh index 0d58138..578eb89 100755 --- a/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/5.0_3PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh index 4d8273c..76dc00a 100755 --- a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh +++ b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_3nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh index 78abc50..35167ce 100755 --- a/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/6.0_4PAA_0Ca_104calcite_1nm_crystal_4nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh b/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh index 1ee1d2c..409bf22 100755 --- a/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh +++ b/submission/input/0-goddard-tests/7.0_4PAA_0Ca_104calcite_2nm_crystal_4nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 7f364de..f116aa4 100755 --- a/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.0_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 3cfe769..2c8bb6e 100755 --- a/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.1_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 50b6b57..43c41f4 100755 --- a/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.2_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 0c8e1f1..87541a3 100755 --- a/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.3_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh index 2654751..bbfacce 100755 --- a/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/4.4_16PAA_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh index 0d67776..bbc1b4a 100755 --- a/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/5.0_16PAAn_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh index e978b51..7532565 100755 --- a/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/6.0_16PVAc_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Ace" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh index 4cef6c2..680a06c 100755 --- a/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/1-model-system/7.0_16PVOH_0Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Alc" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh index 0404631..794fa0c 100755 --- a/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/1.0_1PAA_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh index e560fbf..161b164 100755 --- a/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/2.0_1PAAn_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh index 097d380..35d5b11 100755 --- a/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/3.0_1PVAc_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Ace" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh b/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh index a294f19..fdbf1ac 100755 --- a/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh +++ b/submission/input/2-monomers/4.0_1PVOH_0Ca_104calcite_5nm_crystal_8nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='100' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Alc" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh index c3dc8b3..1677e04 100755 --- a/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/1.0_16PAA_8Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh index 6592430..7fcc856 100755 --- a/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/2.0_16PAA_16Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh index f87766d..d2d2865 100755 --- a/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/3.0_16PAA_32Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh b/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh index 2ea6eda..77065a7 100755 --- a/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/3-ionic-strength/4.0_16PAA_64Ca_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index 0ff58e2..c46dcd4 100755 --- a/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh index f15cd06..ce5660b 100755 --- a/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh index aa83e72..468469e 100755 --- a/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/3.0_64CaCO3_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh index 53396a9..e31e9c4 100755 --- a/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/4.0_16AA_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh index ff90f48..00c5e95 100755 --- a/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/5.0_16An_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh index 4d31c99..86e8ae9 100755 --- a/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/6.0_16Al_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Alc" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh b/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh index 5d60c3e..0d4473d 100755 --- a/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/4-test-systems/7.0_16Ac_104calcite_9nm_crystal_10nm_height.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Ace" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/5-one-opes-params/1.0_lowbarrier3.sh b/submission/input/5-one-opes-params/1.0_lowbarrier3.sh index 1b975aa..2a34551 100755 --- a/submission/input/5-one-opes-params/1.0_lowbarrier3.sh +++ b/submission/input/5-one-opes-params/1.0_lowbarrier3.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/5-one-opes-params/2.0_lowbarrier5.sh b/submission/input/5-one-opes-params/2.0_lowbarrier5.sh index e425224..df960ba 100755 --- a/submission/input/5-one-opes-params/2.0_lowbarrier5.sh +++ b/submission/input/5-one-opes-params/2.0_lowbarrier5.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh b/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh index 589afc8..ef1ff44 100755 --- a/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh +++ b/submission/input/5-one-opes-params/3.0_lowbarrier5_geom370.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh b/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh index 4380da4..61383e5 100755 --- a/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh +++ b/submission/input/5-one-opes-params/4.0_lowbarrier5_geom350.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh b/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh index c5bb9d0..f99474e 100755 --- a/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh +++ b/submission/input/5-one-opes-params/5.0_lowbarrier5_lower305_geom370.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh b/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh index 7131757..aff18af 100755 --- a/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh +++ b/submission/input/5-one-opes-params/6.0_lowbarrier5_lower304_upper374.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh b/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh index dcda3cf..935af24 100755 --- a/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh +++ b/submission/input/5-one-opes-params/7.0_lowbarrier8_lower304_upper374.sh @@ -20,7 +20,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh index 40e41e5..9474d85 100755 --- a/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.0_16paa_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh index a69ea55..8c2c932 100755 --- a/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.1_16paa_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh index 26fff9c..1cdcb8f 100755 --- a/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.2_16paa_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh index aa7940f..7b1873d 100755 --- a/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.3_16paa_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh index 129ca21..e21b915 100755 --- a/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/1.4_16paa_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh index 0709cdf..b1158c9 100755 --- a/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.0_16paan_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh index 2b1d449..27f9bda 100755 --- a/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.1_16paan_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh index 98cf589..1a2eb29 100755 --- a/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.2_16paan_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh index 186410c..57e00a8 100755 --- a/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.3_16paan_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh b/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh index c706b12..ccdba31 100755 --- a/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/2.4_16paan_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh index 1059927..01eb83b 100755 --- a/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.0_32paa_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh index 24f955f..c563ec3 100755 --- a/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.1_32paa_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh index 50483eb..e2d5b44 100755 --- a/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.2_32paa_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh index 00c18f3..091d283 100755 --- a/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.3_32paa_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh index a2c7e12..b24b7c3 100755 --- a/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/3.4_32paa_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh index b7de14e..a08c183 100755 --- a/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.0_32paan_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh index 5f2dc1d..75a2ac8 100755 --- a/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.1_32paan_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh index 85e9afb..7143604 100755 --- a/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.2_32paan_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh index c70662d..fb18afe 100755 --- a/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.3_32paan_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh index 25cf959..133dfed 100755 --- a/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/4.4_32paan_0Ca_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acn" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh index 1eb4856..4c82f41 100755 --- a/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.0_32paa_32CaCl2_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh index adb00b1..63ccc4b 100755 --- a/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.1_32paa_32CaCl2_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh index 8a970b6..310cf33 100755 --- a/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.2_32paa_32CaCl2_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh index fe321f9..eb2edce 100755 --- a/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.3_32paa_32CaCl2_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh b/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh index 3fd5296..4c5bf8d 100755 --- a/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh +++ b/submission/input/6-diffusion-model-systems/5.4_32paa_32CaCl2_12nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh index 16f4360..484aa55 100755 --- a/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/1.0_104calcite_9nm_crystal_10nm_height.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh index 26f4389..ecba063 100755 --- a/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/2.0_64CaCl2_104calcite_9nm_crystal_10nm_height.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh index efab4e1..1f50d78 100755 --- a/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh +++ b/submission/input/7-vacuum-systems/3.0_16AA_104calcite_9nm_crystal_10nm_height.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc} diff --git a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh index c9d31ae..e76cf0f 100755 --- a/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh +++ b/submission/input/7-vacuum-systems/4.0_16paa_0Ca_9nmcrystal.sh @@ -23,7 +23,7 @@ export TEMPERATURE_K='300' # temperature in Kelvin export PRESSURE_BAR='1' # pressure in bar # integration -export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500} +export INTEGRATION_NS='500' # [ns] final simulation time for production run {100, 500, 1000} # polyelectrolyte chemistry export MONOMER="Acr" # Dominant monomer: {Acr, Acn, Asp, Glu, Ace, Alc}