Visual Molecular Dynamics

VMD

Screenshot of VMD 1.8.3.
Original author(s) University of Illinois at Urbana–Champaign
Stable release 1.9.2 / December 2014 (2014-12)
Operating system Mac OS X, Unix, Windows
Type Molecular modelling
License VMD License (distribution-specific)
Website VMD website

Visual molecular dynamics (VMD) is a molecular modelling and visualization computer program.[1] 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 runs on Unix, Apple MacOS X, and Microsoft Windows.[2] VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge.[3]

History

Satellite tobacco mosaic virus molecular graphics produced in VMD and rendered using Tachyon. The scene is shown with a combination molecular surfaces colored by a radial distance, and nucleic acids shown in ribbon representations. The Tachyon rendering uses both direct lighting and ambient occlusion lighting to improve the visibility of pockets and cavities. The VMD axes are shown as a simple example of rendering of non-molecular geometry.

VMD has been developed under the aegis of principal investigator Klaus Schulten in the Theoretical and Computational Biophysics group at the Beckman Institute at the University of Illinois at Urbana–Champaign.[4][5] A precursor program, called VRChem, was developed in 1992 by Mike Krogh, William Humphrey, and Rick Kufrin. The initial version of VMD was written by William Humphrey, Andrew Dalke, Ken Hamer, Jon Leech, and James Phillips.[6] It was released in 1995.[6][7] The earliest versions of VMD were developed for Silicon Graphics workstations and could also run in the CAVE and communicate with a NAMD simulation.[1] VMD was further developed by A. Dalke, W. Humphrey, J. Ulrich in 1995-1996, followed by Sergei Izrailev and J. Stone during 1997-1998. 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.[8] The first version of VMD for the Microsoft Windows platform was released in 1999.[9] In 2001, Justin Gullingsrud, and Paul Grayson, and John Stone added support for haptic feedback devices and further developing the interface between VMD and NAMD for performing interactive molecular dynamics simulations.[10][11] In subsequent developments, Jordi Cohen, Gullingsrud, and Stone entirely rewrote the graphical user interfaces, added built-in support for display and processing of volumetric data,[12] and the use of OpenGL Shading Language.[13]

Interprocess communication

VMD can communicate with other programs via Tcl/Tk.[2]

See also

External links

Wikimedia Commons has media related to VMD.

References

  1. 1 2 Humphrey, William; Dalke, Andrew; Schulten, Klaus (February 1996). "VMD: Visual molecular dynamics". Journal of Molecular Graphics 14 (1): 33–38. doi:10.1016/0263-7855(96)00018-5. PMID 8744570. Retrieved 4 January 2016.
  2. 1 2 "VMD User's Guide Version 1.9.1" (PDF). Massachusetts Institute of Technology. NIH Resource for Macromolecular Modeling and Bioinformatics. Retrieved January 29, 2012.
  3. ↑ "VMD License". Theoretical and Computational Biophysics Group. NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign. Retrieved 4 January 2016.
  4. ↑ Schulten, Klaus. "Department of Health and Human Services Public Health Service National Institutes of Health NIH Resource Biomedical Research Technology Program Annual Progress Report, Grant Number P41 RR05969" (PDF). University of Illinois at Urbana-Champaign. Retrieved 5 January 2016.
  5. ↑ Schulten, Klaus J. "Department of Health and Human Services Public Health Service National Institutes of Health National Center for Research Resources Biomedical Technology Area Annual Progress Report (8/1/10 – 7/31/11), Grant Number P41RR005969" (PDF). University of Illinois at Urbana-Champaign. Retrieved 5 January 2016.
  6. 1 2 "VMD Release History". Theoretical and Computational Biophysics Group. NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign. Retrieved 4 January 2016.
  7. ↑ Bishop, Tom Connor (July 4, 1995). "Announcing the Program VMD, Version 1.0". Computation Chemistry List. CCL.Net.
  8. ↑ "VMD 1.3". Theoretical and Computational Biophysics Group. NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign. Retrieved 4 January 2016.
  9. ↑ "VMD 1.4". Theoretical and Computational Biophysics Group. NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign. Retrieved 4 January 2016.
  10. ↑ Stone, John E.; Gullingsrud, Justin; Grayson, Paul; Schulten, Klaus (2001). "A system for interactive molecular dynamics simulation". 2001 ACM Symposium on Interactive 3D Graphics. New York, NY, USA: ACM. pp. 191–194.
  11. ↑ Dreher, Matthieu; Piuzzi, Marc; Ahmed, Turki; Matthieuten, Chavent; et al. (2013). "Interactive Molecular Dynamics: Scaling up to Large Systems". International Conference on Computational Science, ICCS 2013, Jun 2013, Barcelone, Spain (PDF). New York, NY, USA: Elsevier.
  12. ↑ "VMD 1.8". Theoretical and Computational Biophysics Group. NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign. Retrieved 4 January 2016.
  13. ↑ "VMD 1.8.7". Theoretical and Computational Biophysics Group. NIH Center for Macromolecular Modeling & Bioinformatics University of Illinois at Urbana-Champaign. Retrieved 4 January 2016.
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