Scalable molecular dynamics with NAMD

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kalé, Klaus Schulten

Research output: Contribution to journalReview article

Abstract

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tel scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

Original languageEnglish (US)
Pages (from-to)1781-1802
Number of pages22
JournalJournal of Computational Chemistry
Volume26
Issue number16
DOIs
StatePublished - Dec 2005

Fingerprint

Molecular Dynamics
Molecular dynamics
Molecular graphics
Laptop computers
Pressure control
Grid computing
Temperature control
Personal computers
Free energy
Equations of motion
Electrostatics
Simulation
Software
Sequence Analysis
Force Field
Grid Computing
Potential Function
C++
Costs
Free Energy

Keywords

  • Biomolecular simulation
  • Molecular dynamics
  • Parallel computing

ASJC Scopus subject areas

  • Chemistry(all)
  • Safety, Risk, Reliability and Quality

Cite this

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., ... Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781-1802. https://doi.org/10.1002/jcc.20289

Scalable molecular dynamics with NAMD. / Phillips, James C.; Braun, Rosemary; Wang, Wei; Gumbart, James; Tajkhorshid, Emad; Villa, Elizabeth; Chipot, Christophe; Skeel, Robert D.; Kalé, Laxmikant; Schulten, Klaus.

In: Journal of Computational Chemistry, Vol. 26, No. 16, 12.2005, p. 1781-1802.

Research output: Contribution to journalReview article

Phillips, JC, Braun, R, Wang, W, Gumbart, J, Tajkhorshid, E, Villa, E, Chipot, C, Skeel, RD, Kalé, L & Schulten, K 2005, 'Scalable molecular dynamics with NAMD', Journal of Computational Chemistry, vol. 26, no. 16, pp. 1781-1802. https://doi.org/10.1002/jcc.20289
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E et al. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 2005 Dec;26(16):1781-1802. https://doi.org/10.1002/jcc.20289
Phillips, James C. ; Braun, Rosemary ; Wang, Wei ; Gumbart, James ; Tajkhorshid, Emad ; Villa, Elizabeth ; Chipot, Christophe ; Skeel, Robert D. ; Kalé, Laxmikant ; Schulten, Klaus. / Scalable molecular dynamics with NAMD. In: Journal of Computational Chemistry. 2005 ; Vol. 26, No. 16. pp. 1781-1802.
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