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MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, Amber and other simulation packages.
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, 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.
Start with Learning MDAnalysis.
Then continue with the Quick Start Guide in the User Guide.
The published papers on MDAnalysis contain high-level descriptions of the structures and philosophy of the library together with examples of its use.
To get help, report problems, and just become part of the MDAnalysis community, see Participating.
This Wiki is primarily for developers and specific pages/information that hasn't found another place elsewhere. As a user, you'll probably find what you need in the User Guide or via the MDAnalysis web site.
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 3.9. MDAnalysis has been successfully used on Linux, Mac OS X and Windows.
The MDAnalysis 'Atom' Logo was designed by Christian Beckstein and is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.