pmx: alchemistry in gromacs¶

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling.

Warning: this is a development version of pmx, it is not stable or reliable yet. You are welcome to try/test it and provide feedback, but use at your own risk. The current stable version of pmx can be found here: https://github.com/dseeliger/pmx

pmx is a python library that allows users to setup and analyse molecular dynamics simulations with the Gromacs package. Among its main features are the setup and analysis of alchemical free energy calculations for protein, nucleic acid, and small molecule mutations.

User Documentation

API Reference

Other Tools

For Developers

Developers Guide

Citations¶

If you use pmx in scientific publications, please cite the following papers:

1. Gapsys, S. Michielssens, D. Seeliger, B.L. de Groot. pmx: Automated protein structure and topology generation for alchemical perturbations. J. Comp. Chem 36 (2015), 348-354
1. Seeliger, B.L. de Groot. Protein Thermostability Calculations Using Alchemical Free Energy Simulations. Biophys. J. 98 (2010), 2309-2316

@article{Gapsys2015pmx,
    title = {pmx: Automated protein structure and topology
    generation for alchemical perturbations},
    author = {Gapsys, Vytautas and Michielssens, Servaas
    and Seeliger, Daniel and de Groot, Bert L.},
    journal = {Journal of Computational Chemistry},
    volume = {36},
    number = {5},
    pages = {348--354},
    year = {2015},
    doi = {10.1002/jcc.23804}
}

@article{Seeliger2010pmx,
    title = {Protein Thermostability Calculations Using
    Alchemical Free Energy Simulations},
    author = {Seeliger, Daniel and de Groot, Bert L.},
    journal = {Biophysical Journal},
    volume = {98},
    number = {10},
    pages = {2309--2316},
    year = {2010},
    doi = {10.1016/j.bpj.2010.01.051}
}

License¶

pmx is licensed under the GNU Lesser General Public License v3.0 (LGPL v3).