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.
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Biophys J. 2010 May 19;98(10):2309-16. doi: 10.1016/j.bpj.2010.01.051.
Protein thermostability calculations using alchemical free energy simulations.
Seeliger D1, de Groot BL.