MDPOW 0.8.0

A library for computing solvation/water partitioning coefficients using molecular dynamics simulations

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 coefficients. Currently implemented:

• water-octanol partition coefficient (P_OW)

• water-cyclohexane partition coefficient (P_CW)

Calculations are performed with the Gromacs MD software package [1]. Currently, OPLS-AA, CHARMM/CGENFF, and AMBER/GAFF parameters are supported.

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).

Documentation

• https://mdpow.readthedocs.io

• Tutorial : computing the octanol-water partition coefficient of benzene (uses the example files)

Installation

See INSTALL for detailed instructions. MDPOW currently supports and is tested with Python 3.7 to 3.9.

You will also need Gromacs (currently tested with versions 4.6.5, 2018, 2020, 2021 but 2016 and 2019 should also work).

Development version

If you want to install the development version, get the sources from GitHub (the development branch)

git clone https://github.com/Becksteinlab/MDPOW.git

and Install from the checked out source:

pip install MDPOW/

(Note the trailing slash / to indicate the directory.)

Source code

MDPOW is open source and published under the GNU General Public License v3. Source code is available at https://github.com/Becksteinlab/MDPOW .

Footnotes

[1]

The package is built on top of the GromacsWrapper framework (which is automatically installed).