VMD

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Contents


Authors/Maintainers

VMD is produced by the The Theoretical and Computational Biophysics Group, an NIH Resource for Macromolecular Modeling and Bioinformatics, that develops and distributes free, effective tools (with source code) for molecular dynamics studies in structural biology.

The VMD project is funded by the National Institutes of Health (grant number PHS 5 P41 RR05969).

Primary citation:

  • Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

Summary

VMD is designed for modeling, 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. Modern graphics processing units (GPUs) contain hundreds of arithmetic units and can be harnessed to provide tremendous acceleration for many numerically intensive scientific applications. Beginning with version 1.8.7, VMD supports CUDA for GPU acceleration of electrostatic potential map calculations, for implicit ligand sampling, and for display of molecular orbitals for quantum chemistry visualization.

Features

  • Support for all major computer platforms
  • Support for multicore processors
  • Support for GPU accelerated computation
  • Many excellent VMD tutorials developed locally, and by the research community at large
  • No limits on the number of molecules, atoms, residues or number of trajectory 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)
  • Support for over 60 molecular file formats and data types through an extensive library of built-in file reader/writer plugins and translators
  • VMD includes a multiple sequence alignment plugin, a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids.
  • 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 Tachyon.
  • User-extensible graphical and text-based user interfaces, built-on standard Tcl/Tk and Python scripting languages
  • 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 program architecture and source code
  • Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD in the Theoretical and Computational Biophysics Group at the University of Illinois. See the NAMD WWW home page for more info: 
   http://www.ks.uiuc.edu/Research/namd/
  • VMD works well with projected display systems like the 3-D Projection Facility maintained by the Theoretical and Computational Biophysics Group.
  • VMD can be used to concurrently display and interact with a running NAMD simulation.

Architectural/Functional Overview

  • high level design info, how it works, performance - may be a link, or several links

Overview of VMD flow of execution

Usage Overview

http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/index.html

Dependencies

VMD requires several libraries and programs for various of its functions. In particular, it uses GL or OpenGL based 3-D rendering, and will require that you have the appropriate GL or OpenGL libraries on your system. Other programs are required by some of VMD's optional features.

For a basic install, VMD needs: FLTK 1.1.7, Tcl/Tk 8.4.x and OpenGL. By default, VMD looks for all of the library dependencies in the vmd/lib directory from the source tree. This is because it links against it's own compilations of Tcl/Tk etc, that are known to have fewer bugs than whatever version the vendors may be shipping at any given time.

If you decide to build VMD from source-code, then these libraries must be compiled and installed. Without these libraries and their associated header files, compilation of the VMD source code and some plugins will fail almost immediately. VMD also supports various optional components such as Python, VRPN, and other packages. They must be linkable in a manner similar to the Tcl/Tk and FLTK. VMD has been tested with Python 2.2 and later, and Numeric 24.2. VMD should be buildable with any version of VRPN from 6.00 up to 7.03. More information at: http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html

HP-SEE Applications

Resource Centers

  • IFIN_Bio, RO
  • BG, BG
  • HPCG, BG
  • NCIT-Cluster, RO

Usage by Other Projects and Communities

  • If any

Recommendations for Configuration and Usage

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