Visual Molecular Dynamics

File:Satellite tobacco mosaic virus rendering produced by VMD and Tachyon.jpg. 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 for Advanced Science and Technology, University of Illinois at Urbana–Champaign.{{cite web|last1=Schulten|first1=Klaus|title=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|url=http://www.ks.uiuc.edu/Publications/Reports/nihreport/NIHreport1996.pdf|website=University of Illinois at Urbana–Champaign|access-date=5 January 2016}}{{cite web|last1=Schulten|first1=Klaus J.|title=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|url=http://www.ks.uiuc.edu/Publications/Reports/nihreport/NIHreport2011.pdf|website=University of Illinois at Urbana–Champaign|access-date=5 January 2016}} 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.{{cite web|title=VMD Release History|url=http://www.ks.uiuc.edu/Research/vmd/allversions/release_history.html|website=Theoretical and Computational Biophysics Group|publisher=NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign|access-date=4 January 2016}} It was released in 1995.{{cite web|last1=Bishop|first1=Tom Connor|title=Announcing the Program VMD, Version 1.0|url=http://www.ccl.net/cgi-bin/ccl/message.cgi?1995+07+04+003|website=Computation Chemistry List|publisher=CCL.Net|date=July 4, 1995}} The earliest versions of VMD were developed for Silicon Graphics workstations and could also run in a cave automatic virtual environment (CAVE) and communicate with a Nanoscale Molecular Dynamics (NAMD) simulation. 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.{{cite web|title=VMD 1.3|url=http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/devel.html|website=Theoretical and Computational Biophysics Group|publisher=NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign|access-date=4 January 2016}} The first version of VMD for the Microsoft Windows platform was released in 1999.{{cite web|title=VMD 1.4|url=http://www.ks.uiuc.edu/Research/vmd/vmd-1.4/devel.html|website=Theoretical and Computational Biophysics Group|publisher=NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign|access-date=4 January 2016}} 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.{{cite book|last1=Stone|first1=John E.|last2=Gullingsrud|first2=Justin|last3=Grayson|first3=Paul|last4=Schulten|first4=Klaus|title=2001 ACM Symposium on Interactive 3D Graphics|date=2001|publisher=ACM|location=New York, NY, USA|chapter=A system for interactive molecular dynamics simulation|pages=191–194|chapter-url=http://www.ks.uiuc.edu/Publications/Papers/paper.cgi?tbcode=STON2001}}{{cite book|last1=Dreher|first1=Matthieu|last2=Piuzzi|first2=Marc|last3=Ahmed|first3=Turki|last4=Matthieuten|first4=Chavent|title=International Conference on Computational Science, ICCS 2013, Jun 2013, Barcelone, Spain|date=2013|publisher=Elsevier|location=New York, NY, USA|chapter=Interactive Molecular Dynamics: Scaling up to Large Systems|chapter-url=https://hal.inria.fr/hal-00809024/file/main.pdf|display-authors=etal}} 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,{{cite web|title=VMD 1.8|url=http://www.ks.uiuc.edu/Research/vmd/vmd-1.8/devel.html|website=Theoretical and Computational Biophysics Group|publisher=NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign|access-date=4 January 2016}} and the use of OpenGL Shading Language.{{cite web|title=VMD 1.8.7|url=http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.7/winrelnotes.html|website=Theoretical and Computational Biophysics Group|publisher=NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign|access-date=4 January 2016}}

VMD can communicate with other programs via Tcl/Tk.{{cite web|title=VMD User's Guide Version 1.9.1|url=http://web.mit.edu/vmd_v1.9.1/ug.pdf|website=Massachusetts Institute of Technology|publisher=NIH Resource for Macromolecular Modeling and Bioinformatics|access-date=January 29, 2012}} This communication allows the development of several external plugins that works together with VMD. These plugins increases the set of features and tools of VMD making it one of the most used software in computational chemistry, biology, and biochemistry.

Here is a list of some VMD plugins developed using Tcl/Tk:

• Delphi Force — electrostatic force calculation and visualization{{Cite journal|last1=Li|first1=Lin|last2=Jia|first2=Zhe|last3=Peng|first3=Yunhui|last4=Chakravorty|first4=Arghya|last5=Sun|first5=Lexuan|last6=Alexov|first6=Emil|date=2017-11-15|title=DelPhiForce web server: electrostatic forces and energy calculations and visualization|journal=Bioinformatics|language=en|volume=33|issue=22|pages=3661–3663|doi=10.1093/bioinformatics/btx495|pmid=29036596|pmc=5870670|issn=1367-4803}}
• Pathways Plugin — identify dominant electron transfer pathways and estimate donor-to-acceptor electronic tunneling
• Check Sidechains Plugin — checks and helps select best orientation and protonation state for Asn, Gln, and His side chains
• MultiMSMS Plugin — caches MSMS calculations to speedup the animation of a sequence of frames
• Interactive Essential Dynamics — Interactive visualization of essential dynamics
• Mead Ionize — Improved version of autoionize for highly charged systems
• Andriy Anishkin's VMD Scripts — Many useful VMD scripts for visualization and analysis
• RMSD Trajectory Tool — Development version of RMSD plugin for trajectories
• Clustering Tool — Visualize clusters of conformations of a structure
• iTrajComp — interactive Trajectory Comparison tool
• Swap — Atomic coordinate swapping for improved RMSD alignment
• Intervor — Protein-Protein interface extraction and display
• SurfVol — Measure surface area and volume of proteins{{Cite journal|last1=Ribeiro|first1=João V.|last2=Tamames|first2=Juan A. C.|last3=Cerqueira|first3=Nuno M. F. S. A.|last4=Fernandes|first4=Pedro A.|last5=Ramos|first5=Maria J.|date=2013-12-01|title=Volarea – A Bioinformatics Tool to Calculate the Surface Area and the Volume of Molecular Systems|journal=Chemical Biology & Drug Design|language=en|volume=82|issue=6|pages=743–755|doi=10.1111/cbdd.12197|pmid=24164915|s2cid=45385688|issn=1747-0285}}
• vmdICE — Plugin for computing RMSD, RMSF, SASA, and other time-varying quantities{{Cite journal|last1=Knapp|first1=Bernhard|last2=Lederer|first2=Nadja|last3=Omasits|first3=Ulrich|last4=Schreiner|first4=Wolfgang|date=2010-12-01|title=vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD|journal=Journal of Computational Chemistry|language=en|volume=31|issue=16|pages=2868–2873|doi=10.1002/jcc.21581|pmid=20928849|s2cid=674918|issn=1096-987X}}
• molUP - A VMD plugin to handle QM and ONIOM calculations using the gaussian software{{Cite journal|last1=Fernandes|first1=Henrique|last2=Ramos|first2=Maria João|last3=Cerqueira|first3=Nuno M. F. S. A.|title=molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software|journal=Journal of Computational Chemistry|volume=39|issue=19|pages=1344–1353|doi=10.1002/jcc.25189|pmid=29464735|year=2018|s2cid=3413848}}
• VMD Store - A VMD extensions that helps users to discover, install, and update other VMD plugins.{{Cite journal|last1=Fernandes|first1=Henrique S.|last2=Sousa|first2=Sérgio F.|last3=Cerqueira|first3=Nuno M. F. S. A.|date=2019-11-25|title=VMD Store–A VMD Plugin to Browse, Discover, and Install VMD Extensions|url=https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00739|journal=Journal of Chemical Information and Modeling|language=en|volume=59|issue=11|pages=4519–4523|doi=10.1021/acs.jcim.9b00739|pmid=31682440|s2cid=207893960 |issn=1549-9596}}

{{columns-list|colwidth=30em|

• List of molecular graphics systems
• Comparison of software for molecular mechanics modeling
• Molecular dynamics
• Grace (plotting tool)
• Ascalaph Designer
• Tachyon (software)
• VRPN

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{{reflist}}

{{Commons category|VMD (software)}}

• {{Official website|www.ks.uiuc.edu/Research/vmd}}
• [http://www.nvidia.com/object/vmd_on_tesla.html VMD on GPUs]
• [http://3d-alignment.eu/ Protein workbench STRAP]

{{Chemistry software}}

Category:Molecular modelling software