分子动力学软件选择.docx

分子动力学软件选择.docx

《分子动力学软件选择.docx》由会员分享，可在线阅读，更多相关《分子动力学软件选择.docx（15页珍藏版）》请在冰豆网上搜索。

分子动力学软件选择

分子动力学软件选择

TherearewidelyusedpackageslikeAMBER,CHARMmandX-PLOR

http:

//www.amber.ucsf.edu/amber/amber.html

http:

//yuri.harvard.edu/

http:

//xplor.csb.yale.edu/

CHARMmandX-PLORbothusethesameforcefield.Amber'sisdifferent.

Ifyou'reWintel-bound,youcouldtryHyperchem,whichhasafree

downloadabledemo:

Ithasanicestructurebuildcapability（theotherpackageshave

powerfullanguages,butcanbeintimidatingtonewusers）.

OpenSourceadherentscanfindawealthoffreepackagesatSAL,an

excellentsite:

MypersonalfavouritesareMMTK,EGOandVMD/NAMD.

Icompiledalistoffreeandcommericalprogramsat

modelinginsolutionispossiblee.g.withtheseprograms（tothebestofmy

knowledge）:

commercial:

AMSOL,GROMOS,Titan

free:

GAMESOL,GROMACS,MOIL,OMNISOL,Tinker

Youfindlinkstoalloftheseprogramsat

PAPA（计算粒状物料的三维并行分子动力学计算程序）

【URL】 http:

//www.ica1.uni-stuttgart.de/Research/Software_P3T/papa.html

【作者】 ICA1Group,InstituteofComputerApplications（ICA）oftheUniversityofStuttgart

【语言版本】 English

【收费情况】 免费

【用途】 Characteristic:

dissipativeinteractionforrotating,rough,sphericalparticles

geometryelements:

walls,cylinders,spheres,etcfreelyconfigurable

materialpropertiesofwallsandparticlesfreelyconfigurableforanarbitraynumberofmaterials

objectoriented,writteninC++

fullcheckpointingsupported

severalcompilationoptions:

supportofX11graphics,reductionto2D,debuggingaids,etc.

Applications:

simulationofgranularmedia,silofillingandsteadyflowproblems,spherepackingsofmono-andpolydispersesystem

ProtoMol（分子动力学并行计算软件）

【URL】 http:

//www.nd.edu/~lcls/Protomol.html

【作者】 LCLSGroupattheUniversityofNotreDame

【语言版本】 English

【操作系统】 SunOS5.8,IRIX6.5,Linux2.4,AIX5.1

【收费情况】 免费

【用途】 PROTOMOLisanobject-orientedcomponentbasedframeworkformoleculardynamicssimulations.TheframeworksupportstheCHARMM19and28a2forcefieldsandisabletoprocessPDB,PSF,XYZandDCDtrajectoryfiles.Itisdesignedforhighflexibility,easyextendibilityandmaintenance,andhighperformancedemands,includingparallelization.Thetechniqueofmultipletime-steppinghasbeenusedtoimprovelong-termefficiency,andtheuseoffastelectrostaticforceevaluationalgorithmslikeplainEwald,ParticleMeshEwald,andMultigridsummationfurtherimprovesperformance.LongertimestepsarepossibleusingMOLLY,LangevinMollyandHybridMonteCarlo,Nose-Hoover,andLangevinintegrators.Inaddition,PROTOMOLhasbeendesignedtointeractwithVMD,avisualizationenginedevelopedbytheUniversityofIllinoisthatisusedfordisplayinglargebiomolecularsystemsinthreedimensions.PROTOMOLisfreedistributedsoftware,andthesourcecodeisincluded.

【相关链接】

　　VMD（分子可视化软件）

　　美国圣母大学：

计算生命科学实验室

Claessen站点的分子模型化软件

【URL】 

【简介】

    MolecularModeling

CommercialSoftware

3DViewer:

converts2Dstructuresinto3DwithsimpleMM2

Alchemy2000:

semiempirical,QSAR,Protein,Polymer,LogP

AMPAC:

semiempiricalquantummechanicalprogram

AMSOL:

semiempirical,solvationmodelsforfreeenergiesofsolvationinaqueoussolutionsandinalkanesolvents

PersonalCAChe:

visualizemoleculesin3D,searchforconformations,analyzechemicalreactivityandpredictpropertiesofcompounds

QuantumCAChe:

PersonalCaCheplusmoleculardynamicsandsemi-empiricalMOPACandZINDOquantummechanics

Chem3D:

MOPACandGaussianintegration,ChemProp,...

Gaussian98W:

MP2,MP3,MP4,MP5,HF,CASSCF,GVB,QCISD,BD,CCSD,G1,G2,ZINDO,ONIOMcalculations,DFTexcitedstates,VCDintensities,...

GROMOS:

general-purposemoleculardynamicscomputersimulationpackageforthestudyofbiomolecularsystems

HyperchemSuite:

semiempirical,RMSFit,MoleculePresentations,SequenceEditor,CrystalBuilder,SugarBuilder,ConformationalSearch,QSARProperties,ScriptEditor...（HyperchemPro,HyperchemStd.）

Jaguar:

electronicstructurecalculation

MacroModel:

allowsthegraphicalconstructionofcomplexchemicalstructuresmechanicsanddynamicstechniquesinvacuoorinsolution

MOPAC2000:

thelatestversionofMOPAC

Spartan:

MM,semiempirical,abinitio,DFT,...

Titan:

TITANistheunionofWavefunction'sversatile,easy-to-useinterfacewithfast,computationalalgorithmsfromSchr鰀inger'sJaguar

WinMOPAC:

basedonMOPAC

Shareware/Freeware

3DViewerforISISDraw:

converts2Dstructuresinto3DwithsimpleMM2

Biomer:

onlinejavaapplet,modelbuildersforpolynucleotides（DNA/RNA）,polysaccharidesandproteins,interactivemoleculeeditor,AMBERforce-fieldbasedgeometryoptimization,simulatedannealingwithmoleculardynamics,andtheabilitytosavegif,jpeg,andppmimages

Chem3DNet:

demoversionofChem3D

COLUMBUS:

high-levelabinitiomolecularelectronicstructurecalculations

Dalton:

quantumchemistryprogram

GAMESOL:

calculatefreeenergiesofsolvationbasedonfixed,gas-phasesolutegeometriesinterfacingGAMESS

GAMESS:

GeneralAtomicandMolecularElectronicStructureSystemisageneralabinitioquantumchemistrypackage

GaussianBasisSet:

getanyGaussianbasissetyoucanimagine

GROMACS:

fullyautomatedtopologybuilderforproteins,moleculardynamics,leap-frogintegrator,positionlangevindynamics,normalmodeanalysis,electrostatics,non-equilibriumMD,NMRrefinementwithNOEdata,largenumberofpowerfulanalysistools,...

Hückel:

constructstheHückelmatrix,theprogramsthencalculate,display

MOIL:

molecularmodeling,energyminimizationandmoleculardynamicssimulationforbiomoleculeslikeproteins

Moldy:

moleculardynamicssimulationprogram,liquids,solids,rigidsurfaces

MOPAC:

generalpurposesemiempiricalmolecularorbitalpackageforthestudyofchemicalstructuresandreactions

MOPAC5.08mn:

modifiedversionofMOPAC

NWChem:

quantumpackageforsupercomputersandLinux,SCF,RHF,UHF,DFT,CASSCF,interfacetoPythonprogramminglanguage

OMNISOL:

calculatingfreeenergiesofsolvationfororganicmoleculescontainingH,C,N,O,F,S,Cl,Br,andIinwaterandorganicsolvents

PCGAMESS:

GAMESSfortheIntelcommunity

Q:

moleculardynamicspackagedesignedforfreeenergycalculationsinbiomolecularsystem

Tinker:

molecularmodelingsoftwareisacompleteandgeneralpackageformolecularmechanicsanddynamics

VMD（分子可视化软件）

【URL】 http:

//www.ks.uiuc.edu/Research/vmd/

【作者】 BiophysicsGroup,UniversityofIllinoisatUrbana-Champaign（UIUC）

【语言版本】 English

【收费情况】 免费

【用途】 VMDisamolecularvisualizationprogramfordisplaying,animating,andanalyzinglargebiomolecularsystemsusing3-Dgraphicsandbuilt-inscripting.VMDsupportscomputersrunningMacOS-X,Unix,orWindows,isdistributedfreeofcharge,andincludessourcecode.

VMDisdesignedforthevisualizationandanalysisofbiologicalsystemssuchasproteins,nucleicacids,lipidbilayerassemblies,etc.Itmaybeusedtoviewmoregeneralmolecules,asVMDcanreadstandardProteinDataBank（PDB）filesanddisplaythecontainedstructure.VMDprovidesawidevarietyofmethodsforrenderingandcoloringamolecule:

simplepointsandlines,CPKspheresandcylinders,licoricebonds,backbonetubesandribbons,cartoondrawings,andothers.VMDcanbeusedtoanimateandanalyzethetrajectoryofamoleculardynamics（MD）simulation.Inparticular,VMDcanactasagraphicalfrontendforanexternalMDprogrambydisplayingandanimatingamoleculeundergoingsimulationonaremotecomputer.VMDusesOpenGLtoprovidehighperformance3-Dmoleculargraphics

【相关链接】

　　RasMol:

3D分子结构显示程序

　　PDB文件显示程序KineMage

　　美国伊利诺依大学：

理论生物物理学研究组

　　JMV（Java分子可视化工具）

　　ProtoMol（分子动力学并行计算软件）

ORAC（用于模拟溶剂化生物分子的分子动力学计算程序,意大利佛罗伦萨大学）

【URL】 http:

//www.chim.unifi.it/orac/

【作者】 MassimoMarchiandP.Procacci

【语言版本】 English

【操作系统】 UNIX

【收费情况】 免费

【用途】 ORACisaprogramforrunningclassicalsimulationsofbiomolecules.SimulationscanbecarriedoutintheNVE,NPT,NHP,andNVTthermodynamicensembles.Theintegrationoftheequationsofmotioninanyensemblecanbecarriedoutwithther-RESPAmultipletimestepintegratorandelectrostaticinteractionscanbehandledwiththeSmoothParticleMeshEwaldmethod.

【备注】

    AparallelversionofORAC4.0（MPI/T3E）isavailableuponrequestto:

MassimoMarchi

SectiondeBiophysiquedesProteinesetdesMembranes,

DBCM,DSV,CEA,Centred'Etudes,

Saclay,91191Gif-sur-YvetteCedex,FRANCE

VirtualMolecularDynamicsLaboratory（分子动力学软件）

【URL】 http:

//polymer.bu.edu/vmdl/index.html

【作者】 AmitBansil,LidiaBraunstein

【语言版本】 English

【收费情况】 免费

【用途】 TheVirtualMolecularDynamicsLaboratoryenablesthestudenttovisualizeatomicmotion,manipulateatomicinteractions,andquantitativelyinvestigatetheresultingmacroscopicpropertiesofbiological,chemical,andphysicalsystems.

TheVirtualLaboratoryisasuiteofresearch-basedmoleculardynamicssoftwaretoolsandproject-basedcurriculumguides.Thesoftwaretoolsare:

"SimpleMolecularDynamics（SMD）","UniversalMolecularDynamics",and"Water".

【相关链接】

　　美国波士顿大学聚合物研究中心（可视化模拟）

DL_POLY（分子动力学模拟软件）

【URL】 http:

//www.cse.clrc.ac.uk/msi/software/DL_POLY/

【作者】 W.SmithandT.R.Forester

【语言版本】 English

【收费情况】 免费

DL_POLYissuppliedtoindividualsunderalicenceandisfreeofcosttoacademicscientistspursuingscientificresearchofanon-commercialnature.Agrouplicenceisalsoavailableforacademicresearchgroups.Allrecipientsofthecodemustfirstagreetothetermsofthelicence.

Commercia