分子动力学模拟实例 扩散系数

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 快递客服问题件处理详细方法山木方法pdf计算方法pdf华与华方法下载八字理论方法下载 ：1.计算体系的均方位移（MeansquaredisplacementＭＳＤ），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.Tosetuptheinitialstructures3.Tobuildanamorphouscell ClicktheAmorphousCellbuttonontheModulestoolbarandselectConstructionfromthedropdownlist.buildanamorphouscellbuildanamorphouscell4.Torelaxthecell-DiscoverSetup4.Torelaxthecell--DiscoverMinimizerModules|Discover|Dynamics Therearedifferenttypesofmoleculardynamicssimulationsandtheseareclassifiedbytheensemblenames,NVE,NVT,NPT,andNPH.Thelettersreferto: N=constantnumberofmolesV=constantvolumeE=constantenergyT=constanttemperatureP=constantpressureH=constantenthalpyModules|Discover|Dynamics SelectNVTfromtheEnsembledropdownlistandchangetheTemperatureto3005.Torunandanalyzemoleculardynamics selectNVEfromtheEnsembledropdownlist. ChangetheNumberofstepsto5000.ChangetheTrajectorySaveoptiontoFullandtheFrameoutputeveryto250 Makecell.xtdtheactivedocument.ClickthePlaybuttonontheAnimationtoolbarRight-clickandchooseLabelfromtheshortcutmentoopentheLabeldialog.SelecttheForcefieldTypepropertyandclicktheApplybutton.SelectEdit|AtomSelectionfromthemenubar. ChangetheSelectbyPropertytoForcefieldType.Inthematchestextfield,typeo1oandclicktheSelectbutton.OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.selectoxygenfromtheChoosesetsdropdownlistmeansquaredisplacement(MSD)oftheoxygenatomswithtime TheDiscoverAnalysistoolusestheclient-serverarchitecturetocalculatethemeansquaredisplacement.Anewfolder,cellDiscoMeansquareddisplacement,iscreatedandthecell.xcddocumentwithinthisfoldercontainsaplotofthemeansquaredisplacement(MSD)oftheoxygenatomswithtime.ThevalueoftheMSDforagiventimereportedinthechartistheaverageoveralltimeintervalsofthatlengthandoverallatomsintheset.MSDExpandtheDynamicnodeandselectMeansquareddisplacement Youmustspecifywhichdocumentyouwanttoperformtheanalysison.AlogicaltrajectorydocumentconsistsofoneormoretrajectoriessoyouwillusethistospecifyyourtrajectorydocumentOntheDiscoverAnalysisdialog,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