Practical 15: MDAnalysis

MDAnalysis is an open source Python library that helps you to quickly write your own analysis algorithm for studying trajectories produced by the most popular simulation packages [Michaud-Agrawal2011].

The online documentation together with the interactive python documentation should help you while you are using the library.

DISCLAIMER: Your instructor is one of the main authors of the package and might be overly enthusiastic in promoting it...


[Michaud-Agrawal2011]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
[Beckstein2009]O Beckstein. EJ Denning, JR Perilla, and TB Woolf. Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open/Closed Transitions. J Mol Biol 394 (2009), 160–176. doi:10.1016/j.jmb.2009.09.009

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