pmx: alchemistry in gromacs

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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).

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.. |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