Visual Molecular Dynamics

Visual molecular dynamics (VMD) is a molecular modelling and visualization computer program. VMD is primarily developed as a tool for viewing and analyzing the results of molecular dynamics simulations, but it also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, Renderman, Tachyon, VRML, and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD is available free of charge, and includes source code, but it's under a non-free license.

Additional recommended knowledge

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History

VMD has been developed by the Theoretical and Computational Biophysics group at the University of Illinois and the Beckman Institute. The original version, called VRChem, was developed in 1992 by M. Krogh, W. Humphrey, and R. Kufrin. The initial version of VMD was written by Andrew Dalke, Jeff Ulrich, and William Humphrey and was released in 1995. The earliest versions of VMD were developed for Silicon Graphics workstations and could also run in the CAVE. After the original VMD developers moved on to other careers, Sergei Izrailev took over maintaining the program until 1998. In 1998, John Stone became the main VMD developer, porting VMD to many other Unix operating systems and completing the first full-featured OpenGL version. The first version of VMD for the Microsoft Windows platform was released in 1999. In 2001, Justin Gullingsrud, and Paul Grayson, and John Stone added support for haptic feedback devices and developed an interface between VMD and NAMD for performing interactive molecular dynamics simulations. In subsequent developments, Jordi Cohen, Gullingsrud, and John Stone entirely rewrote the graphical user interfaces, added built-in support for display and processing of volumetric data, and the first use of OpenGL Shading Language.

Interprocess Communication

VMD can communicate with other programs via TCL/TK.

• protein workbench STRAP

See also

• PyMol
• Gabedit
• Molden
• Molekel
• Grace
• Molecular Dynamics