VMD - VISUAL MOLECULAR-DYNAMICS

VMD is a molecular graphics program designed for the display and analy sis of molecular assemblies, in particular biopolymers such as protein s and nucleic acids. VMD can simultaneously display any number of stru ctures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more ''representations,'' in which e ach representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each re presentation are chosen using an extensive atom selection syntax, whic h includes Boolean operators and regular expressions. VMD provides a c omplete graphical user interface for program control, as well as a tex t interface using the Tcl embeddable parser to allow for complex scrip ts 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 pho torealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulatio n trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDS cope, a set of tools for interactive problem solving in structural bio logy, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. V MD is written in C++, using an object-oriented design; the program, in cluding source code and extensive documentation, is freely available v ia anonymous ftp and through the World Wide Web.