|Developer(s)||University of Illinois at Urbana–Champaign: Theoretical and Computational Biophysics Group (TCB), Parallel Programming Laboratory (PPL)|
2.12 / December 22, 2016
|Operating system||Cross-platform: Windows, Linux, macOS, Unix|
|Type||Molecular dynamics simulation|
|License||Proprietary, freeware for noncommercial use|
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms). 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 at 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.
NAMD has an interface to quantum chemistry packages ORCA and MOPAC, as well as a scripted interface to many other quantum packages. Together with Visual Molecular Dynamics (VMD) and QwikMD, NAMD’s interface provides access to hybrid QM/MM simulations in an integrated, comprehensive, customizable, and easy-to-use suite.
NAMD is available as freeware for non-commercial use by individuals, academic institutions, and corporations for in-house business uses.
- Comparison of software for molecular mechanics modeling
- List of free and open-source software packages
- "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 at Urbana-Champaign. Retrieved 1 August 2016.
- "Hybrid QM/MM NAMD". Theoretical and Computational Biophysics Group (TCB). University of Illinois at Urbana-Champaign. Retrieved 26 March 2018.
- "QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts". Scientific Reports. Retrieved 24 May 2016.
- "NAMD goes quantum: an integrative suite for hybrid simulations". Nature Methods. Retrieved 26 March 2018.
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