pmx

NEW PROJECT HAS BEEN MOVED TO GITHUB! -> https://github.com/dseeliger/pmx Introduction pmx (formerly pymacs) has started as a small bunch of classes to read structure files such as pdb or gro and trajectory data in gromacs xtc format. Over the years it has been extended towards a versatile (bio-) molecular structure manipulation package with some additional functionalities, e.g. gromacs file parsers and scripts for setup and analysis of free energy calculations. Citations: D. Seeliger and Bert L. de Groot, Biophys. J. 98(10):2309-2316 (2010) V. Gapsys, S. Michielssens, D. Seeliger, B. L. de Groot. J. Comput. Chem. 2014, DOI: 10.1002/jcc.23804 Purpose I mostly use pmx to write short scripts which perform some changes in pdb files, e.g. changing atom or residue names, applying some geometric transformations or doing some kind of analysis. The critical issue for these things is usually not calculation time but strai