分子动力学模拟实例-扩散系数-7.ppt

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.Ifyoudonothaveastraigh