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OS: Linux, Windows, Mac, .......

License: Freeware

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.

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 thrugh an extensive library of built-in file reader/writer plugins and translators