This is an archival copy of the Visualization Group's web page 1998 to 2017. For current information, please vist our group's new web page.
VMD at NERSC
Table of Contents
- Description
- VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and scripting. The current default version of VMD is 1.8.
- Features
- VMD has a rich set of functionality for performing Visual Molecular Dynamics. A complete list of the functionality, Image Gallery, technical tips, etc., can be found at the main VMD web site.
- Accessing VMD
- VMD is available on NERSC platforms via the modules facility.
- Documentation
- Links to online local documentation (pdf/html format).
- Additional Resources
- Links to the VMD distribution site, supplemental information, a FAQ page.
- Sample Screen Shots.
Description
- 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.
- VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
Features
- No limits on the number of molecules, atoms, residues or number of animation frames, except available memory.
- Many molecular rendering and coloring methods.
- Stereo display capability.
- Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more).
- 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.
- Ability to export displayed graphics to files which may be processed by a number of popular ray tracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Radiance.
- Extensive graphical and text-based user interfaces, which use the Tcl package to provide full scripting capabilities.
- Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis.
- Modular, extensible source code using an object-oriented design in C++, with a programmers guide describing the source code.
- 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 information: http://www.ks.uiuc.edu/Research/namd/
- VMD works well with projected display systems like the 3-D Projection Facility maintained by the Theoretical Biophysics Group.
- VMD can be used to concurrently display and interact with a running MD simulation using NAMD.
Accessing VMD
To access vmd on NERSC platforms, use the modules facility as follows:
% module load vmd
Documentation
Pdf/postscript Documentation
- Programmer's Guide (ps)
- Programmer's Guide (pdf)
- Installation Guide (pdf)
- Vendor Website: Documentation, Links: Release Notes, User's Guide,Installation Guide, Programmer's Guide.
Local Documentation Downloads: (Use shift left-mouse to download files)
Additional Resources
- VMD Homepage.
- Theoretical Biophysics Group Download site.
- VMD 1.7.1 Stereoscopic Display.
- Theoretical Biophysics Group.
- Biomedical Applications of Molecular Dynamics on the TeraGrid.
- Graphics/Visualization software support at NERSC.
- MD Tools.
- Trajectory Playback with VMD.
- Using VMD as a Web/MIME Helper Application.
- Scripting Interface.
- Portable and Intuitive GUI.
- Interfacing with MD Programs (i.e. SIGMA, NAMD).
- Interactive MD and VR Device Support.
- Making Movies with VMD.
Sample Screen Shots
 |
 |