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Protocols

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


Maintainers


  • person_outline Kelly Young
  • person_outline Klaus Schulten

Publication for Visual Molecular Dynamics

VMD citations

 (2023)
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CHAT gene polymorphism rs3810950 is associated with the risk of Alzheimer’s disease in the Czech population

2018
J Biomed Sci
PMCID: 5950140
PMID: 29759072
DOI: 10.1186/s12929-018-0444-2
call_split See protocol

[…] 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. […]

call_split

Structural basis of actin monomer re charging by cyclase associated protein

2018
Nat Commun
PMCID: 5951797
PMID: 29760438
DOI: 10.1038/s41467-018-04231-7
call_split See protocol

[…] 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 […]

call_split

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

2018
J Mol Biol
PMCID: 5958240
PMID: 29660325
DOI: 10.1016/j.jmb.2018.04.006
call_split See protocol

[…] 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 […]

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Clinically relevant mutations in the ABCG2 transporter uncovered by genetic analysis linked to erythrocyte membrane protein expression

2018
Sci Rep
PMCID: 5945641
PMID: 29749379
DOI: 10.1038/s41598-018-25695-z
call_split See protocol

[…] 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. […]

library_books

Discovery of small molecules through pharmacophore modeling, docking and molecular dynamics simulation against Plasmodium vivax Vivapain 3 (VP 3)

2018
PMCID: 5944417
PMID: 29756074
DOI: 10.1016/j.heliyon.2018.e00612

[…] 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 […]

library_books

Air separation with graphene mediated by nanowindow rim concerted motion

2018
Nat Commun
PMCID: 5935753
PMID: 29728605
DOI: 10.1038/s41467-018-04224-6

[…] 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. […]

Citations

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VMD institution(s)
Theoretical Biophysics Group, University of Illinois, Urbana, USA
VMD funding source(s)
This work is supported by grants from the National Institutes of Health (PHS 5 P41 RR05969-04), the National Science Foundation (BIR- 9318159), and the Roy J. Carver Charitable Trust.

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