VMD
VMD is a molecular visualization and analysis tool for the study of biomolecular systems. Can visualize both static molecular structures, as well as molecular dynamics trajectories, as well as run-time visualization of molecular dynamics simulations. VMD supports a wide variety of Unix systems, including SGI, Sun, HP, IBM, Compaq/DEC, Linux, and others. VMD also runs on Windows 95/98/NT. VMD uses hardware accelerated GL/OpenGL rendering, and can also export scenes to external ray tracing programs for high quality rendering. The most recent production version of VMD is 1.3, however VMD 1.4 will be released in a few weeks.
Obtaining VMD: A more complete description of VMD is available via the VMD WWW home page which is located at http://www.ks.uiuc.edu/Research/vmd/
Features: VMD is designed for the visualization 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, 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, 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. This project is funded by the National Institutes of Health and the National Science Foundation.
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