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Protocols

NAMD specifications

Information


Unique identifier OMICS_05085
Name NAMD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/NAMD

Versioning


No version available

Documentation


Maintainer


  • person_outline Kelly Young

Publication for NAMD

NAMD citations

 (882)
call_split

Structural basis for cofilin binding and actin filament disassembly

2018
Nat Commun
PMCID: 5945598
PMID: 29749375
DOI: 10.1038/s41467-018-04290-w
call_split See protocol

[…] ced with Mg2+ and unmodified histidine, respectively, and the N-terminal amine was acetylated. The initial atomic model was flexibly fitted to a cryo-EM density map with the cascade-MDFF protocol, on NAMD 2.12 software. The calculation was performed under harmonic helical symmetry restraints on all atoms except hydrogens, and the solvent effect was modeled with Generalized Born implicit solvent. A […]

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

[…] ed in the purpose of structures from x-ray crystallography plus from MR (magnetic resonance) research. The MD simulation revisions were executed to investigate the reliability of the macromolecule by NAMD tool 2.7. The basis root means square deviation (RMSD) enhanced at the start of the simulation. It is a frequently used measure of the differences between two superimposed atomic coordinates scor […]

library_books

Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue

2018
Sci Rep
PMCID: 5935735
PMID: 29728603
DOI: 10.1038/s41598-018-25479-5

[…] room temperature and pressure, after 200 ps of thermalization. The CHARMM27 force field, was used for the protein and the modified version of the TIP3P water model,,. Calculations were done with the NAMD program. To simulate the effect of single-point mutations of the residues, E182A, Y178A, N40A and H203A that are in the direct vicinity of the dipeptide, the sidechain of the mutated residue was […]

library_books

Dissecting Structure Encoded Determinants of Allosteric Cross Talk between Post Translational Modification Sites in the Hsp90 Chaperones

2018
Sci Rep
PMCID: 5932063
PMID: 29720613
DOI: 10.1038/s41598-018-25329-4

[…] states on protein residues were generated with the WHATIF program and refined by the H++ web server. MD simulations were performed using CHARMM22 force field and the explicit TIP3P water model in the NAMD 2.6 package. […]

library_books

Substrate bound outward open structure of a Na+ coupled sialic acid symporter reveals a new Na+ site

2018
Nat Commun
PMCID: 5931594
PMID: 29717135
DOI: 10.1038/s41467-018-04045-7

[…] protein, GLYCAM06 for the Neu5Ac, the Joung-Chetham parameters for the monovalent ions and LIPID14 for the lipids. The TIP3P model was used to simulate the water. All systems were then minimised with NAMD version 2.10, using conjugate gradient for 10,000 steps. Following minimisation, the systems were gradually heated from 10 to 310 K at a rate of 20 K/15 ps using temperature reassignment. During […]

library_books

Computationally identified novel agonists for GPRC6A

2018
PLoS One
PMCID: 5912754
PMID: 29684031
DOI: 10.1371/journal.pone.0195980

[…] t of 1 ps-1. Particle Mesh Ewald (PME) was used for the calculation of the electrostatic interactions. The trajectory coordinates were written to disk every 2 ps.The MD simulation was performed using NAMD-2.9 (MPI version) []. All simulations used CHARMM-36 parameters for protein, lipids, ions and water molecules []. Three equilibration steps were performed, as follows: 1) the lipid tails were equ […]

Citations

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NAMD institution(s)
Beckman Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA; UMR CNRS/UHP 7565, Université Henri Poincaré, Vandœuvre–lès–Nancy, France; Department of Computer Science and Beckman Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA
NAMD funding source(s)
Funding for the Resource for Macromolecular Modeling and Bioinformatics is provided by the National Institutes of Health grant NIH P41 RR05969.

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