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VMD specifications
Information
| Unique identifier | OMICS_03804 |
|---|---|
| Name | VMD |
| Alternative name | Visual Molecular Dynamics |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux, Mac OS, Windows |
| Programming languages | C++ |
| Computer skills | Advanced |
| Stability | Stable |
| Maintained | Yes |
Versioning
No version available
Documentation
- Documentation: http://www.ks.uiuc.edu/Research/vmd/current/ug.pdf
Maintainers
- person_outline Kelly Young
- person_outline Klaus Schulten
Publication for Visual Molecular Dynamics
VMD: visual molecular dynamics.
VMD citations
(2023)CHAT gene polymorphism rs3810950 is associated with the risk of Alzheimer’s disease in the Czech population
[…] 0T of the same isoform were prepared using ab initio modelling Robetta server (http://robetta.bakerlab.org/) and homology modelling software MODELLER []. Search for hydrogen bond network was done via VMD [], Schrodinger Maestro software (Schrodinger, L. Biologics Suite 2017–1) and PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.) as well as the visualization device. […]
Structural basis of actin monomer re charging by cyclase associated protein
[…] tin, CARP domain, WH2, and CAP1248–474) were prepared using Propka (pKa estimation based on the crystallized complex and determination of protonation states at pH = 6.8), Chimera (placing hydrogens), VMD (protein structure building and visualization), and PyTopol (protein topology conversion from CHARMM to the GROMACS format). In all systems, E454 and H416 of the CARP domain were protonated; N-ter […]
A1603P and K1617del, Mutations in β Cardiac Myosin Heavy Chain that Cause Laing Early Onset Distal Myopathy, Affect Secondary Structure and Filament Formation In Vitro and In Vivo
[…] within Chimera . Generation of a starting structure for the K1617del mutant is described below.Starting structures were energy minimized for 1000 steepest decent steps in vacuum using CHARMM . Using VMD , a 1.5-nm surround of water molecules and Na+ and Cl− ions were then added to neutralize the construct and give a NaCl concentration of ~ 150 mM. A 10,000-step minimization, 0–300 K heating proto […]
Clinically relevant mutations in the ABCG2 transporter uncovered by genetic analysis linked to erythrocyte membrane protein expression
[…] NBD (residues 31–304) structure was dissected from our ABCG5/ABCG8 homology model. Details and validity are described in the Supplementary material. The NBD with the M71V mutation was generated using VMD. […]
Discovery of small molecules through pharmacophore modeling, docking and molecular dynamics simulation against Plasmodium vivax Vivapain 3 (VP 3)
[…] aratus for tiny compounds (SwissParam, http://www.swissparam.ch). It generates parameters that are according to the CHARMM27 field of force (for energy minimization). Ions and water were generated by VMD 1.9.1(Visual Molecular Dynamics) (). The counter ions were positioned for neutralization and TIP3P (Transferable Intermolecular Potential 3P) waters were positioned at arbitrary. The extent of hyp […]
Air separation with graphene mediated by nanowindow rim concerted motion
[…] t the system temperature. Later, the framework was quenched rigid and its energy minimized followed by another equilibration run and collection.All molecular models in the figures were prepared using VMD 1.9.3 and rendered with Tachyon. […]
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