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.
| Developer(s) | University of Illinois Urbana–Champaign: Theoretical and Computational Biophysics Group (TCBG), Parallel Programming Laboratory (PPL) |
|---|---|
| Initial release | 1995 |
| Stable release | 2.14
/ August 5, 2020 |
| Repository | |
| Written in | C++ |
| Operating system | Cross-platform: Windows, Linux, macOS, Unix |
| Platform | x86, x86-64 |
| Available in | English |
| Type | Molecular dynamics simulation |
| License | Proprietary, freeware for noncommercial use |
| Website | www |
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
editReferences
edit- ^ "Flexibility and Interoperability in a Parallel Molecular Dynamics Code" (postscript).
- ^ "NAMD A Parallel Object-Oriented Molecular Dynamics Program" (PDF).
- ^ "NAMD: Scalable Molecular Dynamics". Theoretical and Computational Biophysics Group (TCB). University of Illinois Urbana-Champaign. Retrieved 1 August 2016.
- ^ "Hybrid QM/MM NAMD". Theoretical and Computational Biophysics Group (TCB). University of Illinois Urbana-Champaign. Retrieved 26 March 2018.
- ^ 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.
- ^ 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.
External links
edit
- Official website, at TCB website
- NAMD page at the PPL website
- NAMD on GPUs
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