MDAnalysis and the included algorithms are scientific software that are described in academic publications. Please cite these papers when you use MDAnalysis in published work.

It is possible to automatically generate a list of references for any program that uses MDAnalysis. This list (in common reference manager formats) contains the citations associated with the specific algorithms and libraries that were used in the program.

MDAnalysis library

When using MDAnalysis in published work, please cite the following two papers.

(We are asking you to cite both papers if at all possible because the 2016 paper describes many updates to the original 2011 paper and neither paper on its own provides a comprehensive description of the library. We will publish a complete self-contained paper with the upcoming 1.0 release of MDAnalysis, which will then supersede these two citations.)

Included algorithms

The full list of references for included algorithms is maintained and kept up-to-date as part of the documentation.


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.

The MDAnalysis ‘Atom’ Logo was designed by Christian Beckstein and is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.