分子动力学模拟实例-扩散系数-7.ppt

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1、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、GettingstartedBeginbystartingMaterialsStudioandcreatinganewproject.OpentheNewProjectdialogandenterpolymer_gasasthep

2、rojectname,clicktheOKbutton.Thenewprojectiscreatedwithpolymer_gaslistedintheProjectExplorer.2.Tosetuptheinitialstructures3.TobuildanamorphouscellClicktheAmorphousCellbuttonontheModulestoolbarandselectConstructionfromthedropdownlist.buildanamorphouscellbuildanamorphouscell4.Torelaxthecell-Discov

3、erSetup4.Torelaxthecell--DiscoverMinimizerModules

4、Discover

5、DynamicsTherearedifferenttypesofmoleculardynamicssimulationsandtheseareclassifiedbytheensemblenames,NVE,NVT,NPT,andNPH.Thelettersreferto:N=constantnumberofmolesV=constantvolumeE=constantenergyT=constanttemperatureP=constantpressure

6、H=constantenthalpyModules

7、Discover

8、DynamicsSelectNVTfromtheEnsembledropdownlistandchangetheTemperatureto3005.TorunandanalyzemoleculardynamicsselectNVEfromtheEnsembledropdownlist.ChangetheNumberofstepsto5000.ChangetheTrajectorySaveoptiontoFullandtheFrameoutputeveryto250Makecell.xtdtheactivedocum

9、ent.ClickthePlaybuttonontheAnimationtoolbarRight-clickandchooseLabelfromtheshortcutmentoopentheLabeldialog.SelecttheForcefieldTypepropertyandclicktheApplybutton.SelectEdit

10、AtomSelectionfromthemenubar.ChangetheSelectbyPropertytoForcefieldType.Inthematchestextfield,typeo1oandclicktheSelectbutton.

11、OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.OntheLabeldialogclicktheRemoveAllbuttonandclosethedialog.selectoxygenfromtheChoosesetsdropdownlistmeansquaredisplacement(MSD)oftheoxygenatomswithtimeTheDiscoverAnalysistoolusestheclient-serverarchitecturetocalculatethemeansquaredisplace

12、ment.Anewfolder,cellDiscoMeansquareddisplacement,iscreatedandthecell.xcddocumentwithinthisfoldercontainsaplotofthemeansquaredisplacement(MSD)oftheoxygenatomswithtime.ThevalueoftheMSDforagiventimereportedinthechartistheaverageovera