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1、UniversityofIllinoisatUrbana-ChampaignBeckmanInstituteforAdvancedScienceandTechnologyTheoreticalandComputationalBiophysicsGroupComputationalBiophysicsWorkshopUsingVMDVMDDeveloper:JohnStoneTutorialContributors:AlekAksimentiev,AntonArkhipov,RobertBrunner,JordiCohen,Brijeet
2、Dhaliwal,JohnEargle,JenHsin,FatemehKhalili,EricH.Lee,ZanLuthey-Schulten,PatrickO’Donoghue,ElijahRoberts,AnuragSethi,MarcosSotomayor,EmadTajkhorshid,LeonardoTrabuco,ElizabethVilla,YiWang,DavidWells,DanWright,YingYinMay20112Acurrentversionofthistutorialisavailableathttp://
3、www.ks.uiuc.edu/Training/Tutorials/Jointhetutorial-l@ks.uiuc.edumailinglistforadditionalhelp.CONTENTS3Contents1WorkingwithaSingleMolecule81.1LoadingaMolecule..........................81.2DisplayingtheMolecule.......................91.3GraphicalRepresentations............
4、..........101.3.1Exploringdifferentdrawingstyles..............101.3.2Exploringdifferentcoloringmethods............121.3.3Displayingdifferentselections................131.3.4Creatingmultiplerepresentations..............141.4SequenceViewerExtension.....................151.5Sa
5、vingYourWork..........................171.6TheBasicsofVMDFigureRendering...............181.6.1Settingthedisplaybackground...............181.6.2Increasingresolution.....................181.6.3Colorsandmaterials.....................191.6.4Depthperception...................
6、....211.6.5Rendering...........................232TrajectoriesandMovieMaking252.1LoadingTrajectories.........................252.2MainMenuAnimationTools....................262.3TrajectoryVisualization.......................272.3.1Smoothingtrajectories....................
7、272.3.2Displayingmultipleframes.................272.3.3Updatingselections.....................282.4TheBasicsofMoveMakinginVMD................292.4.1Makingsingle-framemovies.................302.4.2Makingtrajectorymovies..................303ScriptinginVMD323.1TheBasicsofTc
8、lScripting.....................323.2VMDscripting............................343.2.1Loadingmoleculeswith
