分子动力学模拟实例-扩散系数-7

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（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.TobuildanamorphouscellClicktheAmorphousCellbuttonontheModulestoolbarandselectConstructionfromthedropdownlist.buildanamorphouscellbuildanamorphouscell4.Torelaxthecell--DiscoverMinimizerModules|Discover|DynamicsTherearedifferenttypesofmoleculardynamicssimulationsandtheseareclassifiedbytheensemblenames,NVE,NVT,NPT,andNPH.Thelettersreferto:N=constantnumberofmoles

V=constantvolume

E=constantenergy

T=constanttemperature

P=constantpressure

H=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