Editing Visual Molecular Dynamics

{{Short description|Visualization and modelling software}}
{{Infobox software
| name = VMD
| logo = 
| screenshot = Vmd screenshot.png
| screenshot size = 275px
| caption = Screenshot of VMD 1.8.3.
| author = William Humphrey, Andrew Dalke, [[Klaus Schulten]], John Stone
| developer = [[University of Illinois at Urbana–Champaign]]
| released = {{Start date and age|1995|07|04}}
| latest release version = {{wikidata|property|preferred|P348|P548=Q2804309|P348}}
| latest release date = {{wikidata|qualifier|preferred|P348|P548=Q2804309|P577}}
| operating system = [[macOS]], [[Unix]], [[Microsoft Windows|Windows]]
| language = English
| programming language = [[C (programming language)|C]]
| genre = [[Molecular modelling]]
| license = Distribution-specific<ref>[http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.html VMD license]</ref>
| website = {{URL|www.ks.uiuc.edu/Research/vmd}}
}}
[[File:Aerosolized SARS-CoV-2 Virion.png|thumb|350x350px|VMD visualization of a 1-billion atom aerosolized SARS-CoV-2 virion, rendered with [[Tachyon (software)|Tachyon]] on a workstation with 1TB RAM.]]
'''Visual Molecular Dynamics''' ('''VMD''') is a [[molecular modelling]] and [[Visualization (computer graphics)|visualization]] [[computer program]].<ref name=Humphrey>{{cite journal|last1=Humphrey|first1=William|last2=Dalke|first2=Andrew|last3=Schulten|first3=Klaus|title=VMD: Visual molecular dynamics|journal=Journal of Molecular Graphics|date=February 1996|volume=14|issue=1|pages=33–38|doi=10.1016/0263-7855(96)00018-5|pmid=8744570}}</ref> VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. 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 (software)|RenderMan]], [[Tachyon (software)|Tachyon]], Virtual Reality Modeling Language ([[VRML]]), and many others. Users can run their own [[Tcl]] and [[Python (programming language)|Python]] scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on [[Unix]], Apple Mac [[macOS]], and [[Microsoft Windows]].<ref name=UserGuide/> 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.<ref name=License>{{cite web|title=VMD License|url=http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.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}}</ref>

== History ==
[[File:Satellite tobacco mosaic virus rendering produced by VMD and Tachyon.jpg|thumb|350x350px|Satellite tobacco mosaic virus molecular graphics produced in VMD and rendered using [[Tachyon (software)|Tachyon]]. The scene is shown with a combination molecular surfaces colored by a radial distance, and [[nucleic acid]]s 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]].<ref name=RR05969>{{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}}</ref><ref name=P41RR005969>{{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}}</ref> 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.<ref name=Releases>{{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}}</ref> It was released in 1995.<ref name=Releases/><ref name=Bishop>{{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}}</ref> 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.<ref name=Humphrey/> 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.<ref name=VMD1.3>{{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}}</ref> The first version of VMD for the [[Microsoft Windows]] platform was released in 1999.<ref name=VMD1.4>{{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}}</ref> In 2001, Justin Gullingsrud, and Paul Grayson, and John Stone added support for [[Haptic technology|haptic feedback]] devices and further developing the interface between VMD and [[NAMD]] for performing interactive molecular dynamics simulations.<ref name=2001ACM>{{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}}</ref><ref name=Dreher>{{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}}</ref> 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,<ref name=VMD1.8>{{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}}</ref> and the use of [[OpenGL Shading Language]].<ref name=VMD1.8.7>{{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}}</ref>

== Interprocess communication ==
VMD can communicate with other programs via [[Tcl]]/[[Tk (framework)|Tk]].<ref name=UserGuide>{{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}}</ref> 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<ref>{{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}}</ref>
* 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<ref>{{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}}</ref>
* vmdICE — Plugin for computing RMSD, RMSF, SASA, and other time-varying quantities<ref>{{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}}</ref>
* molUP - A VMD plugin to handle QM and ONIOM calculations using the gaussian software<ref>{{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}}</ref>
* VMD Store - A VMD extensions that helps users to discover, install, and update other VMD plugins.<ref>{{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|url-access=subscription}}</ref>

== See also ==
{{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]]
}}

== References ==
{{reflist}}

== External links ==
{{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]]