MDAnalysis documentation

Release:0.15.0
Date:May 16, 2016

MDAnalysis (www.mdanalysis.org) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, LAMMPS, or DL_POLY; it also reads other formats (e.g. PDB files and XYZ format trajectories; see Table of supported coordinate formats for the full list). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol (see Selection exporters).

It allows one to read molecular dynamics trajectories and access the atomic coordinates through NumPy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. Fairly complete atom Selection Commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out in a range of formats.

Source code is available from https://github.com/MDAnalysis/mdanalysis/ under the GNU Public Licence, version 2, together with some additional documentation.

Please report bugs or enhancement requests through the Issue Tracker. Questions can also be asked on the mdnalysis-discussion mailing list.

Citation

When using MDAnalysis in published work, please cite

  • N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319–2327. doi:10.1002/jcc.21787

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.

Thank you!

Indices and tables