Scalable molecular dynamics with NAMD Export

@article{phillips:05, 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 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 . {\copyright} 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1781-1802, 2005}, address = {Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; UMR CNRS/UHP 7565, Universit\'{e} Henri Poincar\'{e}, 54506 Vand{\ae}uvre-l\`{e}s-Nancy, Cedex, France; Department of Computer Science and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801}, author = {Phillips, James C. and Braun, Rosemary and Wang, Wei and Gumbart, James and Tajkhorshid, Emad and Villa, Elizabeth and Chipot, Christophe and Skeel, Robert D. and Kal\'{e}, Laxmikant and Schulten, Klaus}, citeulike-article-id = {449842}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/jcc.20289}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/16222654}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=16222654}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/112102010/ABSTRACT}, doi = {10.1002/jcc.20289}, issn = {1096-987X}, journal = {Journal of Computational Chemistry}, keywords = {dynamics, molecular, software}, month = {December}, number = {16}, pages = {1781--1802}, posted-at = {2009-01-08 22:55:21}, priority = {0}, title = {Scalable molecular dynamics with NAMD}, url = {http://dx.doi.org/10.1002/jcc.20289}, volume = {26}, year = {2005} }

TY - JOUR ID - phillips:05 L3 - citeulike-article-id:449842 N2 - 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 . © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1781-1802, 2005 IS - 16 JF - Journal of Computational Chemistry SN - 1096-987X AD - Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; UMR CNRS/UHP 7565, Université Henri Poincaré, 54506 Vandæuvre-lès-Nancy, Cedex, France; Department of Computer Science and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 EP - 1802 TI - Scalable molecular dynamics with NAMD VL - 26 SP - 1781 KW - dynamics KW - molecular KW - software AU - Phillips, James AU - Braun, Rosemary AU - Wang, Wei AU - Gumbart, James AU - Tajkhorshid, Emad AU - Villa, Elizabeth AU - Chipot, Christophe AU - Skeel, Robert AU - Kalé, Laxmikant AU - Schulten, Klaus PY - 2005/12// UR - http://dx.doi.org/10.1002/jcc.20289 ER -