MDAnalysis Tutorial

MDAnalysis version

≥ 0.18.0

Tutorial release


Last updated

Aug 19, 2020

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 [Gowers2016] [Michaud-Agrawal2011].

This tutorial serves as an introduction to MDAnalysis. It starts out with installing the library and then introduces the key components of the library. It will show you

  • how to load a structure or a MD trajectory;

  • how to select parts of your system;

  • how to work with atoms, residues and molecules through the object-oriented interface of MDAnalysis;

  • how to analyze MD trajectories;

  • how to write out modified trajectories;

  • how to use algorithms in the MDAnalysis.analysis module (intermediate level of difficulty)

The tutorial contains many links to the online documentation , which you can use to learn more about the functions, classes, an methods that are discussed. The online help together with the interactive Python documentation (help(...) or ...? in ipython) should help you while you are using the library.

If you have questions or suggestions please post them in the MDAnalysis User Discussion Group.

Begin the tutorial with How to use this tutorial and use the sidebar for navigation.