VMD User's Guide

Chapter 1IntroductionVMD is a molecular graphics program designed for the interactive visualization and analysis ofbiopolymers such as proteins, nucleic acids, lipids, and membranes. VMD runs on all major Unixworkstations, Apple MacOS X, and Microsoft Windows. Online information about VMD is availablefrom:http://www.ks.uiuc.edu/Research/vmd/List of key VMD features:• General molecular visualizationAt its heart, VMD is a general application for displaying molecules containing any numberof atoms and is similar to other molecular visualization programs in its basic capabilities.VMD reads data files using an extensible plugin system, and supports Babel for conversion ofother formats. User-defined atom selections can be displayed in any of the standard molecularrepresentations. Displayed graphics can be exported to an image file, to a scene file usableby ray tracing programs, or to a geometry description file suitable for use with 3-D printers.• Visualization of dynamic molecular dataVMD can load atomic coordinate trajectories from AMBER, Charmm, DLPOLY, Gromacs,MMTK, NAMD, X-PLOR, and many other simulation packages. The data can be used toanimate the molecule or to plot the change in molecular properties such as angles, dihedrals,interatomic distances, or energies over time.• Visualization of volumetric dataVMD can load, generate, and display, volumetric maps. Supported map formats includeCryoEM maps, electrostatic potential maps, electron density maps, and many other map fileformats.• Interactive molecular dynamics simulationsVMD can be used as a graphical front-end to a live molecular dynamics program running ona remote supercomputer or high-performance workstation. VMD can interactively apply andvisualize forces in an MD simulation as it runs.• Molecular analysis commandsMany commands are provided for molecular analysis. These include commands to extractinformation on sets of atoms and molecules, vector and matrix routines for coordinate manipulation,and functions for computing values such as center of mass and radius of gyration.9