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MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.
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.
A typical usage pattern is to iterate through a trajectory and analyze coordinates for every frame.
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. The papers on MDAnalysis contain high-level descriptions of the structures and philosophy of the library together with examples of its use.
We started a FAQ (frequently asked questions).
The Wiki is primarily for developers and contains guides and notes for development and release, including notes on how to contribute code for users who want to join our open source project.
MDAnalysis also has example scripts and fairly general analysis modules, available as MDAnalysis.analysis — you can use this code as a starting point for your own analysis scripts.
Finally, you can also ask for advice or help on the mdnalysis-discussion mailing list. If you find bugs or want to request enhancements please file a report in the Issue Tracker.
See citing MDAnalysis.
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.