Scalable molecular dynamics with NAMD

Journal of Computational Chemistry - Tập 26 Số 16 - Trang 1781-1802 - 2005
J. C. Phillips1, Rosemary Braun1, Wei Wang1, James C. Gumbart1, Emad Tajkhorshid1, Elizabeth Villa1, Christophe Chipot2, Robert D. Skeel3, Laxmikant V. Kalé3, Klaus Schulten1
1Beckman Institute, University of Illinois at Urbana–Champaign, Urbana, Illinois, 61801
2UMR CNRS/UHP 7565, Université Henri Poincaré, 54506 Vandæuvre-lès-Nancy, Cedex, France
3Department of Computer Science and Beckman Institute, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801

Tóm tắt

AbstractNAMD 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 atwww.ks.uiuc.edu. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1781–1802, 2005

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Journal of Computational Chemistry

Tập 26 Số 16

1781-1802

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