1 Introduction

VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes. Currently VMD runs on any SGI using IRIX 5.2 or higher, but it can also run on Hewlett-Packard workstations and most Linux boxes if you use the Mesa graphics library. Online information about VMD is available from http://www.ks.uiuc.edu/Research/vmd/.

VMD has several features:

• General molecular visualization
  At its heart, this program is a general application for displaying molecules containing any number of atoms. It is similar in basic capabilities to commercial programs such as Quanta and non-commercial programs such as RasMol, XMol, and Ribbons. It can read PDB files or use Babel (if available) to convert other formats automatically. Once loaded, user-defined subsets of the molecule can be displayed in various ways including licorice, ribbons, van der Waal spheres, and molecular surfaces. The display can be saved directly to a postscript file or in a format suitable for use by ray shading programs such as Raster3D, POV, and Rayshade.
• Visualization of dynamic molecular data
  VMD can read molecular trajectories from DCD and Amber files, or it can acquire timesteps from a running molecular dynamics program. The data can be used to animate the molecule or to plot the change in molecular properties such as interatomic distances, angles, or dihedrals over time.
• Display and control of molecular dynamics simulations
  VMD can be used as a graphical front end to a molecular dynamics (MD) program running on a remote supercomputer or high-performance workstation. VMD uses the MDComm software to set up, initiate, and interactively display and control the MD simulation as the simulation 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.
• Support for several input and display (output) devices
  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, including a Polhemus Fastrak. An interface to the the CAVE library has been developed for use in many different types of stereo projection facilities.
• Tcl scripting language
  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.
• Molecular analysis commands
  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.

 
• 1.1 For more information on VMD and MDScope
• 1.2 Contacting the authors
• 1.3 Credits and program reference
• 1.4 Registering VMD
• 1.5 Acknowledgments
• 1.6 Disclaimer