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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 SGI workstations
with IRIX 5.3 or higher, Hewlett-Packard workstations with HP-UX 10.20,
Sun workstations with Solaris 2.6 or higher, IBM RS/6000 workstations with
AIX 4.3, and PC's with RedHat Linux.
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 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.
Next: For more information on
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Justin Gullingsrud
Tue Apr 6 09:22:39 CDT 1999