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.
To properly credit MDAnalysis, please cite both of the following papers. The 2016 paper details significant updates to the 2011 paper, and together they provide a comprehensive description of the library.
R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy, doi:10.25080/majora-629e541a-00e.
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
(If you are reading the HTML version of the paper, have a look at the paper errata. The free PubmedCentral manuscript PMC3144279 has correct code, which can be copied and pasted.)
If you use MDAnalysis in your projects, we encourage you to display our badge. You can use the embed code below that suits your markup:
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The full list of citations for included algorithms is maintained in our documentation and updated regularly.
MDAnalysis was inspired by the Schulten Group’s MDTools for Python.
The DCD reading code originates from VMD’s catdcd.
MDAnalysis is released under the LGPL license, with some third-party code under LGPL-compatible licenses. For instance, the DCD reading code is licensed 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. NumFOCUS as the fiscal sponsor of MDAnalysis holds all rights on the logo (see branding/logos/LICENSE).