NAMD

Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program)[1] is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model (not to be confused with CHARMM). It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms).[2] It has been developed by the collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois Urbana–Champaign.

Nanoscale Molecular Dynamics
Developer(s)University of Illinois Urbana–Champaign: Theoretical and Computational Biophysics Group (TCB), Parallel Programming Laboratory (PPL)
Initial release1995 (1995)
Stable release
2.14 / August 5, 2020 (2020-08-05)
Repository
Written inC++
Operating systemCross-platform: Windows, Linux, macOS, Unix
Platformx86, x86-64
Available inEnglish
TypeMolecular dynamics simulation
LicenseProprietary, freeware for noncommercial use
Websitewww.ks.uiuc.edu/Research/namd

It was introduced in 1995 by Nelson et al. as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores.[3]

NAMD has an interface to quantum chemistry packages ORCA and MOPAC, as well as a scripted interface to many other quantum packages.[4] Together with Visual Molecular Dynamics (VMD) and QwikMD,[5] NAMD's interface provides access to hybrid QM/MM simulations in an integrated, comprehensive, customizable, and easy-to-use suite.[6]

NAMD is available as freeware for non-commercial use by individuals, academic institutions, and corporations for in-house business uses.

See also

References
  1. "Flexibility and Interoperability in a Parallel Molecular Dynamics Code" (postscript).
  2. "NAMD A Parallel Object-Oriented Molecular Dynamics Program" (PDF).
  3. "NAMD: Scalable Molecular Dynamics". Theoretical and Computational Biophysics Group (TCB). University of Illinois Urbana-Champaign. Retrieved 1 August 2016.
  4. "Hybrid QM/MM NAMD". Theoretical and Computational Biophysics Group (TCB). University of Illinois Urbana-Champaign. Retrieved 26 March 2018.
  5. Ribeiro, João V.; Bernardi, Rafael C.; Rudack, Till; Stone, John E.; Phillips, James C.; Freddolino, Peter L.; Schulten, Klaus (2016). "QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts". Scientific Reports. 6: 26536. Bibcode:2016NatSR...626536R. doi:10.1038/srep26536. PMC 4877583. PMID 27216779.
  6. Melo, Marcelo C R.; Bernardi, Rafael C.; Rudack, Till; Scheurer, Maximilian; Riplinger, Christoph; Phillips, James C.; Maia, Julio D C.; Rocha, Gerd B.; Ribeiro, João V.; Stone, John E.; Neese, Frank; Schulten, Klaus; Luthey-Schulten, Zaida (2018). "NAMD goes quantum: an integrative suite for hybrid simulations". Nature Methods. 15 (5): 351–354. doi:10.1038/nmeth.4638. PMC 6095686. PMID 29578535.
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