MDAnalysis Tutorial

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].

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.

Contents

• Installing MDAnalysis
  • Installation methods
    • Local installation
    • Virtual machine
  • Testing the installation
• Preparations
  • Python interpreter
  • Loading MDAnalysis
• Basics
  • Universe and AtomGroup
    • Exercise 1
  • Selections
    • Exercises 2
• Working with AtomGroups
  • Important methods and attributes of AtomGroup
  • Exercises 3
  • Processing AtomGroups
• Trajectory analysis
  • Exercises 4
  • Bells and whistles
• Writing coordinates
  • Single frames
  • Trajectories
    • Example: Protein-only trajectory
    • Example: Saving dynamic per-atom properties in B-factor
• Using the MDAnalysis.analysis modules
  • RMSD
  • Superposition of structure
  • Exercise 5

References

[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

[Seyler2014]

L. Seyler and O. Beckstein. Sampling of large conformational transitions: Adenylate kinase as a testing ground. Molec. Simul. 40 (2014), 855–877. doi: 10.1080/08927022.2014.919497.