When using MDAnalysis in published work, please cite the following two papers:
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 102-109, Austin, TX, 2016. SciPy.
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
Douglas L. Theobald. Rapid calculation of RMSD using a quaternion-based characteristic polynomial. Acta Crystallographica A 61 (2005), 478-480. doi: 10.1107/S0108767305015266
Pu Liu, Dmitris K. Agrafiotis, and Douglas L. Theobald. Fast determination of the optimal rotational matrix for macromolecular superpositions. J. Comput. Chem. 31 (2010), 1561-1563. doi: 10.1002/jcc.21439
If you use the helix analysis algorithm HELANAL in MDAnalysis.analysis.helanal please cite
If you use the GNM trajectory analysis code in MDAnalysis.analysis.gnm please cite
If you use the water analysis code in MDAnalysis.analysis.waterdynamics please cite
If you use the Path Similarity Analysis (PSA) code in MDAnalysis.analysis.psa please cite
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.