NHSE Software Catalog

VMD - Visual Molecular Dynamics

url

http://www.ks.uiuc.edu/Research/vmd/

record_maintainer

Andrew Dalke <dalke@ks.uiuc.edu>

date_of_information

Mon Jul 31 14:14:06 1995

lifn

lifn:nhse:da6ef6a489b9237f63019931414a2891

review_level

Partially reviewed

version

1.0

pubdate

July 1, 1995

author

Bill Humphrey,
Andrew Dalke,
Jon Leech,
Ken Hamer,
Jim Phillips

contact

vmd@ks.uiuc.edu

abstract

VMD is a molecular graphics program designed for the interactive
visualization of bioppolymers such as proteins, nucleic acids,
and lipids and membranes. Its features include:

Molecular visualization - it can read PDB and X-PLOR PSF
files or automatically call Babel for translation of other
types. Parts of molecule can be selected and rendered in
multiple styles including licorice, ribbons, and van der
Waal spheres. Stereo displays are supported. Raster outputs
are available though ray tracing packages like Raster3D.

Visualization of dynamics molecular data - VMD can read
and animate DCD files or acquire the timestep information
from a running molecular dynamics program. The only
supported program is namd (see
http://www.ks.uiuc.edu/Research/namd/)

Display and control of molecular dynamics simulations -
VMD is the visualization component of the MDScope project
which will allow for user directed molecular simulations.

Support for several input and display devices - these include
the UNC tracker library for spatial trackers and the CAVE
library for use in many stereo environments.

Easy to modify and extend -- the source code is documented
and a Programmers guide exists for thos wishing to modify
the C++ code. VMD uses the Tcl script language which
allows for the creation of loops, functions, and other
control structures as well as being extensible in its
own right.

reference

Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kale, L.,
Skeel, R., Schulten, K., and Kufrin, R., "MDScope: A
Visual Computing Environment for Structural Biology"
Computer Physics Communications (1995). (In Press).

environment

Requires GL or NPGL, though we are porting to OpenGL.
Binaries available for SGIs running IRIX 5.x.
Source code is in C++ and compiles on vendor compilers for SGI
and HP. lex and yacc also needed. Not yet tested with gcc.
Highly suggested compiling along with FORMS and Tcl.
Additional optional interfaces include Babel, Raster3D,
Rayshade, POV-Ray, the CAVE, and the UNC tracker library.

copyright

VMD is not public domain software. It is copyright by the
Theoretical Biophysics Group and the University of Illinois,
with all published and unpublished rights reserved. Permission
is granted by the authors to use this software for noncommercial
and nonprofit purposes. Commercial use of this software is
prohibited without explicit consent from the VMD developers.

VMD IS PROVIDED ``AS IS'' WITHOUT WARRANTY OF ANY KIND, EITHER
EXPRESSED OR IMPLIED. THE ENTIRE RISK AS TO THE QUALITY AND
PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE
PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.

comments

User documentation is available at
http://www.ks.uiuc.edu/Research/vmd/ug/ug.html
Programmer documentation is at
http://www.ks.uiuc.edu/Research/vmd/pg/pg.html
Compiling and installation guide is at
http://www.ks.uiuc.edu/Research/vmd/ig/ig.html

keywords

image processing; data visualization; application program;
molecular biology