Visual Molecular Dynamics

History

Interprocess communication

VMD can communicate with other programs via Tcl/Tk. 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
• 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
• vmdICE — Plugin for computing RMSD, RMSF, SASA, and other time-varying quantities
• molUP - A VMD plugin to handle QM and ONIOM calculations using the gaussian software
• VMD Store - A VMD extensions that helps users to discover, install, and update other VMD plugins.

References

References

1. [http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.html VMD license]
2. (February 1996). "VMD: Visual molecular dynamics". Journal of Molecular Graphics.
3. "VMD License". NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign.
4. "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".
5. "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".
6. "VMD Release History". NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign.
7. (July 4, 1995). "Announcing the Program VMD, Version 1.0". CCL.Net.
8. "VMD 1.3". NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign.
9. "VMD 1.4". NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign.
10. (2001). "2001 ACM Symposium on Interactive 3D Graphics". ACM.
11. (2013). "International Conference on Computational Science, ICCS 2013, Jun 2013, Barcelone, Spain". Elsevier.
12. "VMD 1.8". NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign.
13. "VMD 1.8.7". NIH Center for Macromolecular Modeling & Bioinformatics, University of Illinois at Urbana–Champaign.
14. "VMD User's Guide Version 1.9.1". NIH Resource for Macromolecular Modeling and Bioinformatics.
15. (2017-11-15). "DelPhiForce web server: electrostatic forces and energy calculations and visualization". Bioinformatics.
16. (2013-12-01). "Volarea – A Bioinformatics Tool to Calculate the Surface Area and the Volume of Molecular Systems". Chemical Biology & Drug Design.
17. (2010-12-01). "vmdICE: A plug-in for rapid evaluation of molecular dynamics simulations using VMD". Journal of Computational Chemistry.
18. (2018). "molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software". Journal of Computational Chemistry.
19. (2019-11-25). "VMD Store–A VMD Plugin to Browse, Discover, and Install VMD Extensions". Journal of Chemical Information and Modeling.