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1、ScalableMolecularDynamicswithNAMD1111JAMESC.PHILLIPS,ROSEMARYBRAUN,WEIWANG,JAMESGUMBART,1123EMADTAJKHORSHID,ELIZABETHVILLA,CHRISTOPHECHIPOT,ROBERTD.SKEEL,31LAXMIKANTKALE´,KLAUSSCHULTEN1BeckmanInstitute,UniversityofIllinoisatUrbana–Champaign,Urbana,Illinois618012UMRCNRS/UHP7565,Universite´HenriPo
2、incare´,54506Vandœuvre-le`s-Nancy,Cedex,France3DepartmentofComputerScienceandBeckmanInstitute,UniversityofIllinoisatUrbana–Champaign,Urbana,Illinois61801Received14December2004;Accepted26May2005DOI10.1002/jcc.20289PublishedonlineinWileyInterScience(www.interscience.wiley.com).Abstract:NAMDisapara
3、llelmoleculardynamicscodedesignedforhigh-performancesimulationoflargebiomo-lecularsystems.NAMDscalestohundredsofprocessorsonhigh-endparallelplatforms,aswellastensofprocessorsonlow-costcommodityclusters,andalsorunsonindividualdesktopandlaptopcomputers.NAMDworkswithAMBERandCHARMMpotentialfunctions
4、,parameters,andfileformats.Thisarticle,directedtonovicesaswellasexperts,firstintroducesconceptsandmethodsusedintheNAMDprogram,describingtheclassicalmoleculardynamicsforcefield,equationsofmotion,andintegrationmethodsalongwiththeefficientelectrostaticsevaluationalgorithmsemployedandtemperatureandpress
5、urecontrolsused.Featuresforsteeringthesimulationacrossbarriersandforcalculatingbothalchemicalandconformationalfreeenergydifferencesarepresented.ThemotivationsforandaroadmaptotheinternaldesignofNAMD,implementedinCandbasedonCharmparallelobjects,areoutlined.Thefactorsaffectingtheserialandparall
6、elperformanceofasimulationarediscussed.Finally,typicalNAMDuseisillustratedwithrepresentativeapplicationstoasmall,amedium,andalargebiomolecularsystem,highlightingparticularfeaturesofNAMD,forexample,theTclscriptinglanguage.ThearticlealsoprovidesalistofthekeyfeaturesofNAMDanddiscussesthebenefitsofco
7、mbiningNAMDwiththemoleculargraphics/sequenceanalysissoftwareVMDandthegridcomputing/collaboratorysoftwareBioCoRE.NAMDisdistributedfreeofchargewithsourcecodeatwww.ks.uiuc.edu.©2005WileyPeriodicals,Inc.JComputChem26:1781–1802,2
