|Date:||March 27, 2015
MDAnalysis is an object-oriented python toolkit to analyze molecular
dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, or
LAMMPS; 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 http://mdanalysis.googlecode.com 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
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.
If you use the RMSD calculation (MDAnalysis.analysis.rms) or
alignment code (MDAnalysis.analysis.align) that uses the
qcprot module please also cite
- Douglas L. Theobald. Rapid calculation of RMSD using a
quaternion-based characteristic polynomial. Acta
Crystallographica A 61 (2005), 478-480.
- Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast
determination of the optimal rotational matrix for macromolecular
superpositions. J. Comput. Chem. 31 (2010), 1561–1563.
If you use the helix analysis algorithm HELANAL in
MDAnalysis.analysis.helanal please cite
- Bansal M, Kumar S, Velavan R. HELANAL — A program to characterise
helix geometry in proteins. J. Biomol. Struct. Dyn. 17
If you use the GNM trajectory analysis code in
MDAnalysis.analysis.gnm please cite
- Benjamin A. Hall, Samantha L. Kaye, Andy Pang, Rafael Perera, and
Philip C. Biggin. Characterization of Protein Conformational
States by Normal-Mode Frequencies. JACS 129 (2007), 11394–11401.