MDPOW documentation

Release:0.7.0-dev
Date:Nov 13, 2017

MDPOW is a python package that automates the calculation of solvation free energies via molecular dynamics (MD) simulations. In particular, it facilitates the computation of partition coeffcients. Currently implemented:

  • water-octanol partition coefficient (POW)
  • water-cyclohexane partition coefficient (PCW)

Warning

Development is still very much in flux and the documentation is at least partially out of date. If something appears unclear or just wrong, then please ask questions on the MDPOW Issue Tracker.

MD engine

Calculations are performed with the Gromacs molecular dynamics (MD) software package [1]. MDPOW is tested with

  • Gromacs 4.6.x
  • Gromacs 5.1.x
  • Gromacs 2016.x

It should be possible to use any of these Gromacs versions without further adjustments, thanks to the underlying GromacsWrapper library [1].

Force fields

Currently, the OPLS-AA force field parameters are supported out of the box. In principle it is possible to add force fields sets by changing the GMXLIB environment variable and providing appropriate template files but this is currently untested.

A number of different water models are supporte (see mdpow.forcefields.GROMACS_WATER_MODELS).

See also

mdpow.forcefields

Required input

As input, the user only needs to provide a structure file (PDB or GRO) and a Gromacs ITP file containing the parametrization of the small molecule (e.g. from LigandBook or ParamChem).

Indices and tables

Footnotes

[1](1, 2) The package is built on top of the GromacsWrapper framework (which is automatically installed).