vmd教程 forces-tutorial

1TCLFORCES

vmd-eplot.tcl8

fromthecommandline,oropenVMDandsourcethescript leintheTkConsole:

sourceplot.tclCenter of mass

70

60

50

x (Å)40

30

20

10

00500100015002000time (ns)25003000

Figure2:Centerofmassposition

plottedversustime.

8YoushouldseeaplotsimilartoFig.2.Thebeginningofthegraphisquadratic,asweexpect.However,ngevindy-namicsinvolveadampingfactor,ngevindynamicsarecommonlyusedin

NAMDtosimulateatconstanttemperature,inthiscaseinaso-

calledNVTensemble.Thekeywordsbeginningwithlangevinin

theNAMDcon guration lecontrolitssettings.WithoutLangevin

dynamicsactivatedandintheabsenceofanyexternalforces,we

wouldbesimulatingintheNVEensemble,inwhichcaseenergy

ratherthantemperatureisconstant.NAMDalsoincludesconstant-

pressureoptionsforsimulationintheNPTensemble.

9NowopenthetrajectoryinVMD.FirstlaunchVMD,thenopentheTkConsole.Makesureyou’reinthetclForcesFilesdirectory,thentypethecommand

molloadpsfcommon/ubiquitin.psfdcdpush/push.dcd

Ifyoucouldnotproducethetrajectory,thereisasampleoneintheexample-outputdirectory.NoticethattheLangevindynamicspreventtheproteinfrommovingtooquickly.