pmx: alchemistry in gromacs
===========================
|build| |cov|
**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 in the master branch: https://github.com/deGrootLab/pmx
``pmx`` is a python library that allows users to setup and analyse molecular
dynamics simulations with the `Gromacs <http://gromacs.org>`_ package.
Among its main features are the setup and analysis of alchemical free energy
calculations for protein, nucleic acid, and small molecule mutations.
https://degrootlab.github.io/pmx/
Citations
---------
``pmx`` is a research software. If you make use of it in scientific publications, please cite the following papers::
@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).
.. |build| image:: https://travis-ci.org/deGrootLab/pmx.svg?branch=master
:alt: Build Status
:scale: 100%
:target: https://travis-ci.org/deGrootLab/pmx
.. |cov| image:: https://codecov.io/gh/deGrootLab/pmx/branch/develop/graph/badge.svg
:alt: Code coverage
:scale: 100%
:target: https://codecov.io/gh/deGrootLab/pmx
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