diff --git a/docs/namd.rst b/docs/namd.rst index 7178b27..32ae3c7 100644 --- a/docs/namd.rst +++ b/docs/namd.rst @@ -34,3 +34,10 @@ engine. They can be accessed using the following accessor functions: .. include:: ../src/alchemtest/namd/restarted/descr.rst .. autofunction:: alchemtest.namd.load_restarted + +.. _namd_restarted_reversed: + +.. include:: ../src/alchemtest/namd/restarted_reversed/descr.rst + +.. autofunction:: alchemtest.namd.load_restarted_reversed + diff --git a/src/alchemtest/namd/__init__.py b/src/alchemtest/namd/__init__.py index 912e5d0..39e8d70 100644 --- a/src/alchemtest/namd/__init__.py +++ b/src/alchemtest/namd/__init__.py @@ -5,3 +5,4 @@ from .access import load_tyr2ala from .access import load_idws from .access import load_restarted +from .access import load_restarted_reversed diff --git a/src/alchemtest/namd/access.py b/src/alchemtest/namd/access.py index d344d17..85e121d 100644 --- a/src/alchemtest/namd/access.py +++ b/src/alchemtest/namd/access.py @@ -73,3 +73,26 @@ def load_restarted(): return Bunch(data=data, DESCR=fdescr) + + +def load_restarted_reversed(): + """Load the NAMD IDWS dataset, run from lambda = 1 -> 0, with interruptions and restarts. + + Returns + ------- + data : Bunch + Dictionary-like object, the interesting attributes are: + + - 'data' : the data files by alchemical leg + - 'DESCR': the full description of the dataset + + """ + + module_path = dirname(__file__) + data = {'both': glob(join(module_path, 'restarted_reversed', 'restarted_reversed*.fepout.bz2'))} + + with open(join(module_path, 'restarted_reversed', 'descr.rst')) as rst_file: + fdescr = rst_file.read() + + return Bunch(data=data, + DESCR=fdescr) diff --git a/src/alchemtest/namd/restarted_reversed/descr.rst b/src/alchemtest/namd/restarted_reversed/descr.rst new file mode 100644 index 0000000..ad8791a --- /dev/null +++ b/src/alchemtest/namd/restarted_reversed/descr.rst @@ -0,0 +1,38 @@ +NAMD: free energy of tyrosine to alanine in vacuo +================================================= + +Free energy change from mutating a Tyr into Ala in vacuo. +Uses Interleaved Double-Wide Sampling (Hénin and Brannigan). +Each lambda window was run separately, and NAMD was interrupted +and restarted multiple times, such that one window may span +multiple fepout files. + +Derived from NAMD FEP Tutorial, available at: +https://www.ks.uiuc.edu/Training/Tutorials/namd/FEP/ + +This calculation was run from lambda = 1.0 to lambda = 0.0, +because it is possible for an IDWS calculation in NAMD to be +run this way. + +Notes +----- +Data Set Characteristics: + :Number of Legs: 1 (forward mutation with IDWS sampling) + :Number of Windows: 11 + :Length of Windows: 50 ps + :System Size: 57 atoms + :Temperature: 300 K + :Alchemical Pathway: Mutation of Tyr into Ala using hybrid molecule. + Nonbonded interactions of perturbed atoms are scaled + with their environment. + :Missing Values: None + :Energy unit: kcal/mol + :Time unit: step + :Date: September 2021 + :Donor: Thomas T. 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('forward', ), (2,)), - (load_restarted, ('both', ), (15,)) + (load_restarted, ('both', ), (15,)), + (load_restarted_reversed, ('both', ), (19,)) ]) def dataset(self, request): return super(TestNAMD, self).dataset(request)