VMD "Visual Molecular Dynamics" 1.2 Released
stone john e
jestone at staff.uiuc.edu
Fri Aug 14 22:27:03 EST 1998
VMD "Visual Molecular Dynamics" 1.2 Release Announcement
The Theoretical Biophysics group at the University of Illinois and the
Beckman Institute For Advanced Science and Technology is happy to
announce the availability of version 1.2 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 IBM, HP, Linux, Sun, and SGI
Unix systems. The documentation 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:
Changes to VMD 1.2 since VMD 1.1:
o Many updates to VMD documentation
o VMD now supports OSF1/Digital Unix 4.x on DEC Alpha with OpenGL or Mesa
o Dihedral angles are now reported in the proper range
o Various small bug fixes, and portability enhancements
-- 1.2 beta 4
o Improved display of 3-D axis labels "X","Y","Z".
o Fixed POV, POV3, Art, Raster3D, and Rayshade renderer export codes.
o Fixed the "write" function found in the "edit animation" dialog.
o VMD runs in the Cave simulator now.
-- 1.2 beta 3
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 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
-- 1.2 beta 2
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 implementations
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 Typing in a command without arguments will print a help message
o Added more commands to Tcl scripting interface
o Many bug fixes
-- 1.2 beta 1
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, etc.
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 remote computer.
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 more).
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 an MD simulation
using NAMD. The two programs, along with the intermediary communcations
package (called MDComm) constitute the 'MDScope' interactive environment.
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)
vmd at ks.uiuc.edu
August 1, 1998
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