分子动力学模拟实例-扩散系数-7.ppt
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分子动力学模拟实例-扩散系数-7.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、Gettingstarted,BeginbystartingMaterialsStudioandcreatinganewproject.OpentheNewProjectdialogandenterpolymer_gasastheprojectname,clicktheOKbutton.Thenewprojectiscreatedwithpolymer_gaslistedintheProjectExplorer.,2.Tosetuptheinitialstructures,3.Tobuildanamorphouscell,ClicktheAmorphousCellbuttonontheModulestoolbarandselectConstructionfromthedropdownlist.,buildanamorphouscell,buildanamorphouscell,4.Torelaxthecell-DiscoverSetup,4.Torelaxthecell-DiscoverMinimizer,Modules|Discover|Dynamics,Therearedifferenttypesofmoleculardynamicssimulationsandtheseareclassifiedbytheensemblenames,NVE,NVT,NPT,andNPH.Thelettersreferto:
N=constantnumberofmolesV=constantvolumeE=constantenergyT=constanttemperatureP=constantpressureH=constantenthalpy,Modules|Discover|Dynamics,SelectNVTfromtheEnsembledropdownlistandchangetheTemperatureto300,5.Torunandanalyzemoleculardynamics,selectNVEfromtheEnsembledropdownlist.ChangetheNumberofstepsto5000.ChangetheTrajectorySaveoptiontoFullandtheFrameoutputeveryto250Makecell.xtdtheactivedocument.ClickthePlaybuttonontheAnimationtoolbar,Right-clickandchooseLabelfromtheshortcutmentoopentheLabeldialog.SelecttheForcefieldTypepropertyandclicktheApplybutton.,SelectEdit|AtomSelectionfromthemenubar.,ChangetheSelectbyPropertytoForcefieldType.Inthematchestextfield,typeo1oandclicktheSelectbutton.OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.,OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.,selectoxygenfromtheChoosesetsdropdownlist,meansquaredisplacement(MSD)oftheoxygenatomswithtime,TheDiscoverAnalysistoolusestheclient-serverarchitecturetocalculatethemeansquaredisplacement.Anewfolder,cellDiscoMeansquareddisplacement,iscreatedandthecell.xcddocumentwithinthisfoldercontainsaplotofthemeansquaredisplacement(MSD)oftheoxygenatomswithtime.ThevalueoftheMSDforagiventimereportedinthechartistheaverageoveralltimeintervalsofthatlengthandoverallatomsintheset.,MSD,ExpandtheDynamicnodeandselectMeansquareddisplacement,Youmustspecifywhichdocumentyouwanttoperformtheanalysison.Alogicaltrajectorydocumentconsistsofoneormoretrajectoriessoyouwillusethistospecifyyourtrajectorydocument,OntheDiscoverAnalysisdialog,selectoxygenfromtheChoosesetsdropdownlist.ClicktheAnalyzebuttonandclosethedialog.,6.Toexportdataandcalculatethediffusivity,Thefinalpartofthistutorialinvolvestheuseofanexternalspreadsheetorchartingpackage.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,
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- 分子 动力学 模拟 实例 扩散系数