Tutorial: Using VMD for visualizing proteins | Learning | Beckstein Lab

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Tutorial: Using VMD for visualizing proteins

Tutorial: Using VMD for visualizing proteins

In this short tutorial (which is part of the class PHY 542: Topics in Biophysics I ) we will learn to use VMD (“Visual Molecular Dynamics”) to

  • visualize a protein
  • perform standard analysis tasks such as superposition by optimizing the root mean square distance
  • visualize and analyze a molecular dynamics trajectory
  • make publication quality images
  • make fancy movies

Getting started

  1. Download and install VMD (registration is required but the software is free and available for Linux, Mac OS X, and Windows)
  2. Start the PHY542: VMD Tutorial

More…

  1. PHY542: Analysing MD Simulations with VMD Tutorial
  2. PHY542: Structural Bioinformatics Tutorial (using VMD and other web tools and databases)

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