MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, Amber or DL_POLY; it also reads other formats (e.g. PDB files and XYZ format trajectories; see the 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 for more details).
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. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written out.
All source code is available under the GNU General Public License, version 2 (or an open source licence compatible with GPLv2) from github.com/MDAnalysis and the Python Package index pypi.python.org/pypi/MDAnalysis.
To install the latest stable release, use pip:
To run the test cases and examples, also install the unit tests (about 20 MiB in size):
The MDAnalysis Tutorial serves as an introduction to the library and there are other Tutorials available, too.
See the Online Documentation for more information on how to use MDAnalysis and the available documentation on the Wiki. The paper on MDAnalysis contains a high-level description of the structure and philosophy of the library together with examples of its use.
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. PMCID:PMC3144279
Please also see the list of included algorithms with additional citations.
MDAnalysis was originally inspired by the Schulten Group’s MDTools for Python, and the DCD reading code is derived from VMD’s catdcd. MDAnalysis is GPL licensed, except for some 3rd party code that is included under GPL-compatible licenses; for instance the dcd reading code is under the UIUC Open Source Licence. See the files AUTHORS and LICENSE in the distribution for details.
Some time-critical routines are written in C or cython and require a working C compiler. The minimum required version of Python is 2.7. MDAnalysis has been successfully used on Linux and Mac OS X.
The MDAnalysis ‘Atom’ Logo was designed by Christian Beckstein and is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.