17. References¶
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.
17.1. Citations for the whole MDAnalysis library¶
When using MDAnalysis in published work, please cite [Michaud-Agrawal2011] and [Gowers2016].
(We are currently 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.)
Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf, and Oliver Beckstein. Mdanalysis: a toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10):2319–2327, 2011. doi:10.1002/jcc.21787.
Richard J. Gowers, Max Linke, Jonathan Barnoud, Tyler J. E. Reddy, Manuel N. Melo, Sean L. Seyler, Jan Domański, David L. Dotson, Sébastien Buchoux, Ian M. Kenney, and Oliver Beckstein. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. Proceedings of the 15th Python in Science Conference, pages 98–105, 2016. 00152. URL: https://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html (visited on 2020-02-05), doi:10.25080/Majora-629e541a-00e.