Difference between revisions of "Mdanalysis"
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Latest revision as of 19:49, 12 August 2022
Description
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).
Environment Modules
Run module spider mdanalysis to find out what environment modules are available for this application.
System Variables
- HPC_MDANALYSIS_DIR - installation directory
- HPC_MDANALYSIS_BIN - executable directory
Citation
If you publish research that uses mdanalysis you have to cite it as follows:
When using MDAnalysis in published work, please cite Michaud-Agrawal2011 and Gowers2016.
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.