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 and Table of Supported Topology Formats for details). It can write most of the coordinate formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMOL (see Selection exporters).
MDAnalysis 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 that integrates well with the wider Python ecosystem. 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://www.mdanalysis.org under the GNU Public Licence, version 2, together with the online documentation. Packages can be downloaded from https://pypi.org/project/MDAnalysis/ or installed/upgraded via PyPI using pip:
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]
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 70 MB of molecular dynamics trajectories and simulation system structures it is not included with the library itself.
When using MDAnalysis in published work, please cite the following two papers:
- R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
- 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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