James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid,
Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and
Klaus Schulten.
Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry, 26:1781-1802, 2005.
(PMC: 2486339))
PHIL2005
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 Tcl 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.
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