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.
amber	Amber molecular dynamics simulation datasets.
namd	NAMD molecular dynamics simulation datasets.
gomc	GOMC Monte Carlo 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
=========================

Benzene in water, alchemically turned into benzene in vacuum separated from 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
    :License: `CC0
              <https://creativecommons.org/publicdomain/zero/1.0/>`_
              Public Domain Dedication

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.