NAMD protocols

NAMD specifications


Unique identifier OMICS_05085
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


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  • person_outline Kelly Young <>

Publication for NAMD

NAMD IN pipelines

PMCID: 5745081
PMID: 29280731
DOI: 10.7554/eLife.30483.037

[…] proportional to the observed em density gradients. mdff runs were set up using vmd (humphrey et al., 1996) and used the charmm36m force field (huang et al., 2017). simulations were carried out using namd (phillips et al., 2005) in vacuum at a temperature of 300k for 500 ps. forces corresponding to em density gradients were coupled using an mdff scaling factor ξ of 0.3. the mdff runs […]

PMCID: 4313061
PMID: 25685792
DOI: 10.1155/2015/487298

[…] protocol is the same as that in our previous studies [28–30] we only list some major features here. both of the unbiased md and the tmd simulations were performed using the parallel md code namd 2.7b1 [50]. for all amino acids, their standard protonation states were considered, that is, the states as for ph 7. after an equilibration procedure [28–30] the md simulations were performed […]

PMCID: 4313061
PMID: 25685792
DOI: 10.1155/2015/487298

[…] procedure [28–30] the md simulations were performed with a 1 fs time step in an npt ensemble at 310 k and 1.013 bar. the functional rotation was enforced using tmd [34] (built-in module of namd) which allows inducing conformation changes between two known states. in the present investigation different parts of the protein were steered using this approach. the force constant per atom […]

PMCID: 4337239
PMID: 25755662
DOI: 10.3389/fpls.2015.00091

[…] (see modeling nad+-bound atsdh)., ten nanosecond trajectories were simulated for the generated models of nad+- bound atsdh, and nad+- bound atsdh in complex with sorbitol, ribitol, or xylitol, using namd 2.8 (phillips et al., 2005) and the force field amberff99sb (hornak et al., 2006). systems were prepared with ambertools 1.5 (case et al., 2010). in the case of the polyols, the parameters […]

PMCID: 4346626
PMID: 25698059
DOI: 10.1038/ncomms7341

[…] was replaced by the crystal structure of denv3 e protein, as it has a shorter loop than denv2. both procedures were done using coot51. the molecular dynamic flexible fitting52 was used together with namd53 and vmd54 for cryo-em map-guided molecular dynamic simulation to optimize the fit of the molecules. symmetry restraints were applied to avoid clashes between neighbouring molecules […]

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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