VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, and lipids and membranes. Currently VMD runs on any SGI running IRIX 5.2 or higher, but it can also run on HPs with the NPGL graphics library (available from Portable Graphics), or on IBM AIX workstations. Online information about VMD is available from http://www.ks.uiuc.edu/Research/vmd/.
VMD has several features:
VMD can read molecular trajectories from a DCD file or acquire the timesteps from a running molecular dynamics program. The data can be used to animate the molecule or to plot the change in interatomic distances, angles, or dihedrals over time.
VMD can be used as a graphical front end to a molecular dynamics (MD) program running on a remote supercomputer or high-performance workstation. It uses the MDComm software to set up, initiate, and interactively display and control the MD simulation as it is running. The user can disconnect from the simulation and let it continue, reattach to a running simulation, or halt the MD program. Any number of simulations may be simultaneously displayed and controlled by a single VMD session.
A number of different visual display and control systems are supported in addition to the usual monitor, keyboard, and mouse. The UNC tracker library is used to get position and orientation information from a wide variety of spatial input devices, included a Polhemus Fastrak. An interface to the the CAVE library has been developed for use in many different types of stereo projection facilities.
VMD uses the freely available Tcl scripting language for processing text commands. This is a very common and popular language which contains variables, loops, subroutines, and much more. The TclX and Tcl-DP extension packages have been included to improve the usefulness of the language.
Many new Tcl commands have been added for doing molecular analysis. These include methods to extract information about a set of atoms and molecules, vector and matrix routines for coordinate manipulation, and functions for computing values like the center of mass and radius of gyration.
VMD is the visualization component of MDScope , a computational environment for structural biology and interactive molecular dynamics.