Basic usage

All datasets in alchemtest are accessible via load_* functions, organized in submodules by the software package that generated them. The current set of submodules are:

gmx	Gromacs molecular dynamics simulation datasets.

As an example, we can access the Gromacs: Benzene in water dataset with:

>>> from alchemtest.gmx import load_benzene
>>> bz = load_benzene()

and use the resulting Bunch object to introspect what this dataset includes. In particular, it features a DESCR attribute with a human-readable description of the dataset:

>>> print(bz.DESCR)
Gromacs: Benzene in water
=========================

Notes
-----
Data Set Characteristics:
    :Number of Legs: 2 (Coulomb, VDW)
    :Number of Windows: 5 for Coulomb, 16 for VDW
    :Length of Windows: 40ns

    :Missing Values: None
    :Creator: \I. Kenney
    :Donor: Ian Kenney (ian.kenney@asu.edu)
    :Date: March 2017

Benzene in water, alchemically turned into benzene in vacuum separated from water

This dataset was generated using `MDPOW <https://github.com/Becksteinlab/MDPOW>`_, with
the `Gromacs <http://www.gromacs.org/>`_ molecular dynamics engine.

as well as the dataset itself:

>>>  bz.data.keys()
['VDW', 'Coulomb']

which consists in this case of two alchemical legs, each having several files. For this dataset each file happens to correspond to a simulation sampling a particular \(\lambda\):

>>> bz.data['Coulomb']
['/usr/local/python3.6/site-packages/alchemtest/gmx/benzene/Coulomb/0000/dhdl.xvg.bz2',
 '/usr/local/python3.6/site-packages/alchemtest/gmx/benzene/Coulomb/0250/dhdl.xvg.bz2',
 '/usr/local/python3.6/site-packages/alchemtest/gmx/benzene/Coulomb/0500/dhdl.xvg.bz2',
 '/usr/local/python3.6/site-packages/alchemtest/gmx/benzene/Coulomb/0750/dhdl.xvg.bz2',
 '/usr/local/python3.6/site-packages/alchemtest/gmx/benzene/Coulomb/1000/dhdl.xvg.bz2']

These paths can be read by any appropriate parser for further analysis. For this particular dataset, see alchemlyb.parsing.gmx for a good set of parsers.