Tutorial: MDAnalysis | Learning | Beckstein Lab

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Tutorial: MDAnalysis

Tutorial: MDAnalysis

MDAnalysis is a Python library for the analysis of particle-based computer simulations, in particular molecular dynamics simulations1. If you are new to MDAnalysis or want a refresher on how to use it (and pick up a few tips and tricks) then you might be interested in this introductory tutorial 2.

It covers

  • installing MDAnalysis on your own computer (or using a Virtual Machine with a full MDAnalysis installation)
  • loading data into a Universe object
  • working with AtomGroup objects and performing selections
  • analyzing trajectories
  • using functions from the MDAnalysis.analysis module
Start the tutorial…

Notes

  1. a N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. J Comp Chem, 32 :2319–2327, 2011. doi: 10.1002/jcc.21787.
  2. a The tutorial grew out of a lesson in the course Simulation Approaches to Bio- and Nanophysics where we had a short introduction to MDAnalysis

Discuss: “Tutorial: MDAnalysis”

August 18, 2013 at 11:49 pm #

Hi,
The tutorials provided in this page are very informative. Thanks for the effort. If possible, could you please extend the tutorial on MD Analysis package (like how to write code for analyzing 3D density in connection with RDF graph…etc).

Thank you
Venkat

June 19, 2014 at 1:23 pm #

@Venkat,

Your questions are best asked on the MDAnalysis user mailing list .

Note that there is a whole module for 3D densities available: MDAnalysis.analysis.density that allows you to read/write and process densities.

Best wishes,
Oliver

Posted by  Oliver Beckstein

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