NAMD protocols

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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

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  • person_outline Kelly Young <>

Publication for NAMD

NAMD in pipelines

 (14)
2017
PMCID: 5449183
PMID: 28504641
DOI: 10.7554/eLife.24303.028

[…] in a bilayer of 509 popc lipids and hydrated with 150 mm kcl electrolyte, resulting in a box of ~14.6 × 14.6 × 10 nm3 (195,255 atoms) in size. the simulations were performed using gromacs 5.0 and namd 2.9 with a length of 400 ns and 240 ns, respectively. simulations of adp-bound ktrab are described at the end of the following section., in the mdff simulations, the homology model of ktrb2a8b2 […]

2016
PMCID: 4731802
PMID: 26823026
DOI: 10.1038/srep19940

[…] systems consisted of approximately 160,000 atoms (full-length complex), 85,000 atoms (lbd heterodimer), 60,000 atoms (pparγ-lbd monomer) and 40,000 (apo-hre)., simulations were performed with namd by applying periodic boundary conditions and an integration time-step of 2.0 fs. all bonds involving non-polar hydrogens were constrained at their equilibrium length using the settle algorithm, […]

2016
PMCID: 4917966
PMID: 27329693
DOI: 10.1038/ncomms11984

[…] results from the computational mesh. all the fe computational analyses were conducted using a cpu 2.4 ghz, 8-gigabyte ram and at the maximum run time of ∼5 h., all md simulations were performed with namd2.10 (ref. ). visual md (vmd), pymol and ucsf chimera were used for all visualizations. the three-dimensional structure of e. coli mscl and +5g mutant ecmscl were generated based on the crystal […]

2016
PMCID: 4933972
PMID: 27381287
DOI: 10.1038/srep29502

[…] technique was used for the electrostatic calculations. the van der waals and short-range electrostatics were cut off at 12.0 å with switch at 10.0 å. the metadynamics simulations were carried out in namd to study the transitions between the intersected and parallel α9 dimers, with the assumption that the transition between two conformations is reversible. the sampling bias was applied to two […]

2016
PMCID: 5242315
PMID: 27802580
DOI: 10.1002/prot.25207

[…] with adaptive poisson‐boltzmann solver (apbs) package in 0.1m kcl. surface cavities were calculated using the 3d‐surfer server with the visgrid algorithm.93–95, md simulations were performed with namd on resources provided by the ou supercomputing center for education and research (oscer) at the university of oklahoma. system preparation, visualization and initial trajectory analyses […]


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NAMD in publications

 (792)
PMCID: 5945598
PMID: 29749375
DOI: 10.1038/s41467-018-04290-w

[…] 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. […]

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

[…] worn was hf/6-31g (d) (hartree-fock/6-31gaussian), and was according to different qm/mm (quantum mechanics/molecular mechanics) ways ()., the molecular dynamic (md) simulation of vp-3 was done by namd 2.7 (nanoscale molecular dynamics) with the charmm27 field of force and the on top of mentioned parameterized compounds to be used during this field of force (; ; ). all vp-3 md simulations […]

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

[…] 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., we also employed the formalism of the discrete molecular dynamics (dmd) simulations– to simulate hsp90 structures (fig. ). in the dmd approach, the protein structures were modeled […]

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

[…] 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. […]

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

[…] 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 […]


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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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