Using VMD: an introductory tutorial

Curr Protoc Bioinformatics. 2008 Dec:Chapter 5:Unit 5.7. doi: 10.1002/0471250953.bi0507s24.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Computational Biology / methods*
  • Computer Simulation*
  • Internet
  • Models, Molecular*
  • Molecular Conformation
  • Phylogeny
  • Protein Conformation
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Sequence Alignment
  • Software*
  • User-Computer Interface

Substances

  • Proteins