diff --git a/docs/namd.rst b/docs/namd.rst index 02c851e..feaf481 100644 --- a/docs/namd.rst +++ b/docs/namd.rst @@ -15,9 +15,16 @@ engine. They can be accessed using the following accessor functions: .. autosummary:: load_tyr2ala + load_idws .. _namd_tyr2ala: .. include:: ../src/alchemtest/namd/tyr2ala/descr.rst .. autofunction:: alchemtest.namd.load_tyr2ala + +.. _namd_idws: + +.. include:: ../src/alchemtest/namd/idws/descr.rst + +.. autofunction:: alchemtest.namd.load_idws diff --git a/src/alchemtest/namd/__init__.py b/src/alchemtest/namd/__init__.py index 65e5325..c8f7805 100644 --- a/src/alchemtest/namd/__init__.py +++ b/src/alchemtest/namd/__init__.py @@ -3,3 +3,4 @@ """ from .access import load_tyr2ala +from .access import load_idws diff --git a/src/alchemtest/namd/access.py b/src/alchemtest/namd/access.py index cb1b921..d43221a 100644 --- a/src/alchemtest/namd/access.py +++ b/src/alchemtest/namd/access.py @@ -30,3 +30,24 @@ def load_tyr2ala(): return Bunch(data=data, DESCR=fdescr) +def load_idws(): + """Load the NAMD IDWS dataset. + + 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 = {'forward': [join(module_path, 'idws', 'quickidws.fepout.bz2']} + + with open(join(module_path, 'idws', 'descr.rst')) as rst_file: + fdescr = rst_file.read() + + return Bunch(data=data, + DESCR=fdescr) diff --git a/src/alchemtest/namd/idws/descr.rst b/src/alchemtest/namd/idws/descr.rst new file mode 100644 index 0000000..4671e59 --- /dev/null +++ b/src/alchemtest/namd/idws/descr.rst @@ -0,0 +1,33 @@ +NAMD: free energy of dummy ethane to ethane "mutation" in aqueous solution +========================================================================== + +Free energy change from mutating an ethane molecule into an ethane molecule, +turning a H atom into a methyl group and conversely. +Expected free energy is zero, however the dataset is tiny (sufficient for +testing purposes). +Uses Interleaved Double-Wide Sampling (Hénin and Brannigan). + +Notes +----- +Data Set Characteristics: + :Number of Legs: 1 (forward mutation in water with IDWS sampling) + :Number of Windows: 11 + :Length of Windows: 500 fs (each window interspersed with 100 fs equilibration) + :System Size: 1030 atoms + :Temperature: 300 K + :Pressure: 1 bar + :Alchemical Pathway: dummy mutation of ethane into ethane using dual topology + hybrid molecule. Nonbonded interactions of perturbed + atoms are scaled with their environment. + :Theoretical Free Energy difference: 0 + :Missing Values: None + :Energy unit: kcal/mol + :Time unit: step + :Date: May 2021 + :Donor: J Hénin + :License: `CC0 `_ + Public Domain Dedication + +This dataset was generated using the `NAMD +`_ molecular dynamics +engine. diff --git a/src/alchemtest/namd/idws/quickidws.fepout.bz2 b/src/alchemtest/namd/idws/quickidws.fepout.bz2 new file mode 100644 index 0000000..9ade136 Binary files /dev/null and b/src/alchemtest/namd/idws/quickidws.fepout.bz2 differ