Introduction

VMD [1] is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes. VMD runs on all major Unix workstations, Apple MacOS X, and Microsoft Windows. Online information about VMD is available from:
http://www.ks.uiuc.edu/Research/vmd/


List of key VMD features:

• General molecular visualization
  At its heart, VMD is a general application for displaying molecules containing any number of 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 of other formats. User-defined atom selections can be displayed in any of the standard molecular representations. Displayed graphics can be exported to an image file, to a scene file usable by ray tracing programs, or to a geometry description file suitable for use with 3-D printers.

• Visualization of dynamic molecular data
  VMD can load atomic coordinate trajectories from AMBER, Charmm, DLPOLY, Gromacs, MMTK, NAMD, X-PLOR, and many other simulation packages. The data can be used to animate the molecule or to plot the change in molecular properties such as angles, dihedrals, interatomic distances, or energies over time.

• Visualization of volumetric data
  VMD can load, generate, and display, volumetric maps. Supported map formats include CryoEM maps, electrostatic potential maps, electron density maps, and many other map file formats.

• Interactive molecular dynamics simulations
  VMD can be used as a graphical front-end to a live molecular dynamics program running on a remote supercomputer or high-performance workstation. VMD can interactively apply and visualize forces in an MD simulation as it runs.

• Molecular analysis commands
  Many commands are provided for molecular analysis. These include commands to extract information 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.

• Tcl and Python scripting languages
  VMD uses the freely available Python and Tcl scripting languages for processing text commands. These popular languages which contain variables, loops, subroutines, and much more. VMD also uses the Tk Toolkit - a simple user interface toolkit that interfaces with Tcl.

• Easy to extend
  VMD is written in C and C++ and employs object-oriented design. VMD implements a plugin interface for extending its file format support and for general purpose extensions in functionality.

• Support for multimodal input and various display systems
  A number of different visual display and control systems are supported in addition to the usual monitor, keyboard, and mouse. The VRPN library is used to get position and orientation information from a wide variety of spatial input devices, including magnetic trackers, haptic (force feedback) devices, Spaceballs, etc. VMD works with WireGL and Chromium on tiled display walls, and immersive VR environments via compiled-in CAVE and FreeVR support.