Clone this wiki locally
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.
Availability and Installing
See the Online Documentation for more information on how to use MDAnalysis and the TableOfContents for a general overview of 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.
See citing MDAnalysis.
Historical, Technical and Artistic Remarks
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.