Software:NAMD
| Developer(s) | University of Illinois Urbana–Champaign: Theoretical and Computational Biophysics Group (TCB), Parallel Programming Laboratory (PPL) |
|---|---|
| Initial release | 1995 |
| Stable release | 2.14
/ August 5, 2020 |
| 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 |
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.
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
- ↑ "Flexibility and Interoperability in a Parallel Molecular Dynamics Code" (postscript). http://www.ks.uiuc.edu/~brunner/Papers/SIAMWS98.ps.
- ↑ "NAMD A Parallel Object-Oriented Molecular Dynamics Program". http://bionum.cs.purdue.edu/NHGD96.pdf.
- ↑ "NAMD: Scalable Molecular Dynamics". University of Illinois Urbana-Champaign. http://www.ks.uiuc.edu/Research/namd/.
- ↑ "Hybrid QM/MM NAMD". University of Illinois Urbana-Champaign. http://www.ks.uiuc.edu/Research/qmmm/.
- ↑ 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. doi:10.1038/srep26536. PMID 27216779. Bibcode: 2016NatSR...626536R.
- ↑ Melo, Marcelo C R.; Bernardi, Rafael C.; Rudack, Till; Scheurer, Maximilian; Riplinger, Christoph; Phillips, James C.; Maia, Julio D C.; Rocha, Gerd B. et al. (2018). "NAMD goes quantum: an integrative suite for hybrid simulations". Nature Methods 15 (5): 351–354. doi:10.1038/nmeth.4638. PMID 29578535.
External links
- , at TCB website
- NAMD page at the PPL website
- NAMD on GPUs
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