分子动力学模拟实例-扩散系数-7PPT资料.ppt

分子动力学模拟实例-扩散系数-7PPT资料.ppt

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分子动力学模拟实例聚合物中分子扩散系数的计算模拟分子动力学做扩散系数有两种方法：

@#@1.计算体系的均方位移（Meansquaredisplacement），然后根据Einstein关系求得扩散系数；@#@2.计算体系的速度自关联函数（Velocityauto-correlationfunctionVACF）然后再通过Green-kubo关系计算体系的扩散系数1、GettingstartedBeginbystartingMaterialsStudioandcreatinganewproject.OpentheNewProjectdialogandenterpolymer_gasastheprojectname,clicktheOKbutton.Thenewprojectiscreatedwithpolymer_gaslistedintheProjectExplorer.2.Tosetuptheinitialstructures3.TobuildanamorphouscellClicktheAmorphousCellbuttonontheModulestoolbarandselectConstructionfromthedropdownlist.buildanamorphouscellbuildanamorphouscell4.Torelaxthecell-DiscoverSetup4.Torelaxthecell-DiscoverMinimizerModules|Discover|DynamicsTherearedifferenttypesofmoleculardynamicssimulationsandtheseareclassifiedbytheensemblenames,NVE,NVT,NPT,andNPH.Thelettersreferto:

@#@N=constantnumberofmolesV=constantvolumeE=constantenergyT=constanttemperatureP=constantpressureH=constantenthalpyModules|Discover|DynamicsSelectNVTfromtheEnsembledropdownlistandchangetheTemperatureto3005.TorunandanalyzemoleculardynamicsselectNVEfromtheEnsembledropdownlist.ChangetheNumberofstepsto5000.ChangetheTrajectorySaveoptiontoFullandtheFrameoutputeveryto250Makecell.xtdtheactivedocument.ClickthePlaybuttonontheAnimationtoolbarRight-clickandchooseLabelfromtheshortcutmentoopentheLabeldialog.SelecttheForcefieldTypepropertyandclicktheApplybutton.SelectEdit|AtomSelectionfromthemenubar.ChangetheSelectbyPropertytoForcefieldType.Inthematchestextfield,typeo1oandclicktheSelectbutton.OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.selectoxygenfromtheChoosesetsdropdownlistmeansquaredisplacement（MSD）oftheoxygenatomswithtimeTheDiscoverAnalysistoolusestheclient-serverarchitecturetocalculatethemeansquaredisplacement.Anewfolder,cellDiscoMeansquareddisplacement,iscreatedandthecell.xcddocumentwithinthisfoldercontainsaplotofthemeansquaredisplacement（MSD）oftheoxygenatomswithtime.ThevalueoftheMSDforagiventimereportedinthechartistheaverageoveralltimeintervalsofthatlengthandoverallatomsintheset.MSDExpandtheDynamicnodeandselectMeansquareddisplacementYoumustspecifywhichdocumentyouwanttoperformtheanalysison.AlogicaltrajectorydocumentconsistsofoneormoretrajectoriessoyouwillusethistospecifyyourtrajectorydocumentOntheDiscoverAnalysisdialog,selectoxygenfromtheChoosesetsdropdownlist.ClicktheAnalyzebuttonandclosethedialog.6.ToexportdataandcalculatethediffusivityThefinalpartofthistutorialinvolvestheuseofanexternalspreadsheetorchartingpackage.Youwilluseittocheckwhetherthecalculationofthemeansquaredisplacementhasbeensuccessfulandthentocalculatethediffusivitycoefficientfromthemeansquaredisplacement.Youshouldcopyandpastethechartdocumentintoyourchosenspreadsheetpackage.Right-clickintheplot,andselectCopyfromtheshortcutmenu.Openanewspreadsheet,right-clickinthespreadsheetandselectPastefromtheshortcutmenu.Atthispointinarealcalculation,youwouldchecktoseeifyourcalculationhasproducedreliableresults.Youcandothisbyplottinglog（MSD）againstlog（time）and,ifyourcalculationhasconverged,youshouldobtainastraightline.Ifyoudonothaveastraightline,youshouldruntheproductionstageofthecalculationagain.PlotMSDvs.time.Calculatethelineofbestfitofthegraphusinglinearregression,y=ax+b.Notedowntheslope,a.D=a/6