分子动力学模拟实例-扩散系数-7.ppt
- 文档编号:2644852
- 上传时间:2022-11-05
- 格式:PPT
- 页数:24
- 大小:1.80MB
分子动力学模拟实例-扩散系数-7.ppt
《分子动力学模拟实例-扩散系数-7.ppt》由会员分享,可在线阅读,更多相关《分子动力学模拟实例-扩散系数-7.ppt(24页珍藏版)》请在冰豆网上搜索。
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
- 配套讲稿:
如PPT文件的首页显示word图标,表示该PPT已包含配套word讲稿。双击word图标可打开word文档。
- 特殊限制:
部分文档作品中含有的国旗、国徽等图片,仅作为作品整体效果示例展示,禁止商用。设计者仅对作品中独创性部分享有著作权。
- 关 键 词:
- 分子 动力学 模拟 实例 扩散系数