Using VMD: An introductory tutorial

Jen Hsin, Anton Arkhipov, Ying Yin, John E. Stone, Klaus Schulten

Research output: Contribution to journalReview articlepeer-review


VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assem-blies, 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.

Original languageEnglish (US)
Pages (from-to)5.7.1-5.7.48
JournalCurrent Protocols in Bioinformatics
Issue numberSUPPL. 24
StatePublished - 2008
Externally publishedYes


  • Animation
  • Interactive visualization
  • Molecular dynamics visualization
  • Molecular modeling

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry


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