Visualizing and analysing Molecular Dynamics trajectories with VMD¶

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 We will use data from [Beckstein2009] as well as an unpublished trajectory.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.

Contents¶

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

References¶

Indices and tables¶

• Index
• Search Page