UNIT 5.7 Using VMD: An Introductory Tutorial

  1. Jen Hsin1,2,
  2. Anton Arkhipov1,2,
  3. Ying Yin1,2,
  4. John E. Stone2,
  5. Klaus Schulten1,2

Published Online: 1 DEC 2008

DOI: 10.1002/0471250953.bi0507s24

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Hsin, J., Arkhipov, A., Yin, Y., Stone, J. E. and Schulten, K. 2008. Using VMD: An Introductory Tutorial. Current Protocols in Bioinformatics. 24:5.7:5.7.1–5.7.48.

Author Information

  1. 1

    Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois

  2. 2

    Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois

Publication History

  1. Published Online: 1 DEC 2008
  2. Published Print: DEC 2008


VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step-by-step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins. Curr. Protoc. Bioinform. 24:5.7.1-5.7.48. © 2008 by John Wiley & Sons, Inc.


  • molecular modeling;
  • molecular dynamics visualization;
  • interactive visualization;
  • animation