pmx-biobb 2.0.0

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

pmx: alchemistry in gromacs
===========================

|build| |cov|

**PMX_BIOBB DISTRIBUTION VERSION**: 2.0.0
**Based on the PMX Icolos branch commit**: https://github.com/deGrootLab/pmx/commit/80f4f8a1552c37e3d926f950d91db77cd4dea9cf

**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