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 <>

NAMD article

NAMD citations

PMCID: 4313061

[…] 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: 3634009

[…] human tlr2 mutants were homology modelled according to the known crystal structure of the tlr2 tir domain [12]. molecular dynamics simulation of all of the human tlr2 mutants was performed using the namd2.9 and vmd1.9.1 software programmes. the software programme pymol was used to construct the molecular surface charges for all of the human tlr2 mutants., differences between wild-type human tlr2 […]

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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