MDAnalysis documentation

Release:0.8.0 Date:January 20, 2014

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 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

Included algorithms

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 (2000), 811–819

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.

Thanks!

Contents

• 1. Overview over MDAnalysis
• 2. Selection Commands
• 3. Analysis modules
• 4. Topology modules
• 5. Coordinates modules
• 6. Selection exporters
• 7. Core modules
• 8. KDTree module

Indices and tables

• Index
• Module Index
• Search Page