VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Mol-ecules are displayed as one or more “representations,” in which each representation embodies a particular rendering method and coloring scheme Jor a selected subset of atoms.The atoms displayed in each representation are chosen us-ing an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported,which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from ,files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools .for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to con-nect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the pro-gram, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.