Visualizing and analysing Molecular Dynamics trajectories with VMD


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This tutorial provides a short introduction to basic use of the VMD (“Visual Molecular Dynamics”) software to visualize and analyze molecular dynamics (MD) trajectories. It is part of the ASU course PHY 542/NAN 542 — Topics in Biophysics I.

For a quick introduction on using VMD look at Protein visualization and analysis with VMD. We will use data from [Beckstein2009] as well as an unpublished trajectory.

Basics of MD simulations can be found in [FrenkelSmit], [Mura2014] and in the lecture notes.


We are going to work through the individual sections in order. Use the navigation links in menu bar to move forward and backwards.

Learning Objectives

  • loading of dynamics trajectories
  • viewing a trajectory
  • use of RMSFitting tools
  • analysis of dynamic collective variables


[FrenkelSmit]D. Frenkel and B. Smit. Understanding Molecular Simulations. Academic Press, San Diego, 2002.
[Mura2014]C. Mura and C. E. McAnany. An introduction to biomolecular simulations and docking. Molecular Simulation, 40 (2014), 732–764. doi:10.1080/08927022.2014.935372
[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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