VMD-"Visual Molecular Dynamics" 1.2 beta 3 available!
Fri Jun 26 11:25:32 EST 1998
Announcing version 1.2b3 release of VMD
The Theoretical Biophysics group at the University of Illinois and the
Beckman Institute would like to announce the availability of version
1.2b3 of the program VMD, a package for the vizualization and analysis
of biomolecular systems. This software is being made available to the
structural biology research community free of charge, and includes the
source code for VMD, documentation, and precompiled binaries for SGIs,
HPs, Solaris 2, and Linux. The documentation (still being updated)
includes an installation guide, a users guide, and a programmers guide
for interested researchers. VMD also provides on-line help through
the use of an external HTML viewer.
A full description of VMD is available via the VMD WWW home page:
New in this version
o VMD now supports AIX 4.x with the native AIX OpenGL implementation
o OpenGL rendering speed has been improved by 2-5x on several platforms
o OpenGL version now correctly supports stereo-in-a-window
o OpenGL/GL versions are now able to interoperate with
VMD scripts created in by one or the other.
o Upgraded some builds to use newer XForms libraries,
which fix some GUI/Mouse bugs
o VMD upgraded to compile with the 2.6c release of the CAVE libraries
o VMD code now builds with much pickier C++ compilers (i.e. HP aCC)
o New Linux binary distributions have working file browser now.
o New Linux RPM style binary distribution
o New HPUX10-OpenGL binaries for Visualize-FX hardware accelerators
o New AIX4-OpenGL binaries for IBM OpenGL hardware accelerators
o Many bug fixes
Version 1.2b2 features
o VMD has been ported to Sun Solaris 2.
o Upgraded to support Linux RedHat 5.0
o OpenGL support works with native HP-UX and Sun OpenGL
o Added Tk support and upraded to Tcl/Tk 8.0
o Upgraded to Babel 1.6
o Added support for MSMS, a program for calculating molecular surfaces
o Added support for Grasp file format
o For most commands, typing in a command without arguments will
print a help message
o Added more commands to Tcl scripting interface
o Many bug fixes
Version 1.2b1 features
o This biggest improvement in version 1.2b1 support for
platforms other than GL-based SGIs. In addition to the full
source and SGI binary distributions, VMD is now available
for HP-UX (tested under 9 and 10) and Linux.
o Greatly enhanced Tcl scripting commands for performing
molecular analysis, writing scripts, developing tutorials,
o New rendering styles, a fast (and cheap) solvent
accessible surface and C-alpha and P trace method, and
improvements to the existing styles.
o New output renderer formats: Postscript, VRML and STL (a
o Support for Amber structure and animation file formats
============= Basic information about VMD =================
VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies,
etc. It may be used to view more general molecules, as VMD can read
standard Protein Data Bank (PDB) files and display the contained
structure. VMD provides a wide variety of methods for rendering and
coloring a molecule: simple points and lines, CPK spheres and
cylinders, licorice bonds, backbone tubes and ribbons, cartoon
drawings, and others. VMD can be used to animate and analyze the
trajectory of a molecular dynamics (MD) simulation. In particular,
VMD can act as a graphical front end for an external MD program by
displaying and animating a molecule undergoing simulation on a
The program has many features, which include:
o No limits on the number of molecules, atoms, residues or
number of animation frames, excepting available memory.
o Many molecular rendering and coloring methods.
o Stereo display capability.
o Extensive atom selection syntax for choosing subsets of atoms for
display (includes boolean operators, regular expressions, and
o Integration with the program 'Babel' which allows VMD to read many
molecular data file formats. Even without the use of Babel,
VMD can read PDB files, as well as CHARMM- and X-PLOR compatible
binary DCD files and X-PLOR compatible PSF files.
o Ability to write the current image to a file which may be
processed by a number of popular raytracing and image rendering
packages, including POV-Ray, Rayshade, Raster3D, and Radiance.
o Extensive graphical and text-based user interfaces, which use the
Tcl package to provide full scripting capabilities.
o Extensions to the Tcl language which enable researchers to write
their own routines for molecular analysis
o Modular, extensible source code using an object-oriented design in
C++, with a programmer's guide describing the source code
o Integration with the program NAMD, a fast, parallel, and scalable
molecular dynamics program developed in conjunction with VMD
in the Theoretical Biophysics Group at the University of Illinois.
See the NAMD WWW home page for more info:
VMD can be used to set up and concurrently display a MD simulation
using NAMD. The two programs, along with the intermediary
communcations package (called MDComm) constitute the 'MDScope'
The software is available for downloading from
Please email any questions to vmd at ks.uiuc.edu.
VMD, NAMD, and the entire MDScope environment are part of
an ongoing project within the Theoretical Biophysics group
to help provide free, effective tools for molecular dynamics
studies in structural biology. For more information, see
http://www.ks.uiuc.edu/Research/MDScope/. This project is
funded by the National Institutes of Health (grant number
PHS 5 P41 RR05969) and the Roy J. Carver Charitable Trust.
vmd at ks.uiuc.edu
June 25, 1998
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