Using VMD: An Introductory Tutorial

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.