MDAnalysis (www.mdanalysis.org) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, LAMMPS, DL_POLY and other packages; it also reads other formats (e.g., PDB files and XYZ format trajectories; see Table of supported coordinate formats and Table of Supported Topology Formats for the full lists). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol (see Selection exporters).
module spider mdanalysis to find out what environment modules are available for this application.
- HPC_MDANALYSIS_DIR - installation directory
- HPC_MDANALYSIS_BIN - executable directory
If you publish research that uses mdanalysis you have to cite it as follows:
MDAnalysis also contains specific algorithms and whole analysis modules whose algorithms have also been published in the scientific literature. Please make sure to also reference any Citations for included algorithms and modules in published work.