MDAnalysis 0.13.0

An object-oriented toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.

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 the Table of Supported Coordinate Formats for details). 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.

Availability

Source code is available from http://www.mdanalysis.org under the GNU Public Licence, version 2, together with the online documentation. Packages can be downloaded from

http://pypi.python.org/pypi/MDAnalysis/

or installed/upgraded via PyPI (using either easy_install or pip):

easy_install -U MDAnalysis
pip install --upgrade MDAnalysis

By default MDAnalysis does not install every dependency needed to run every analysis available in the analysis module or read netcdf Amber trajectories. To install and update these dependencies as well run.

pip install –upgrade ‘MDAnalysis[analysis, AMBER]

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

In order to run the Unit Tests it is also necessary to install a separate package MDAnalysisTests containing the test and test data. As it contains about 20 MB of molecular dynamics trajectories and simulation system structures it is not included with the library itself.

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

For citations of included algorithms and sub-modules please see the references.

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