vmd教程 forces-tutorial

1TCLFORCES

6Nowrunthesimulation:

namd2rot-a.namd>rot-a.log

Thisshouldagaintakejustafewminutes.12

7Plottheanglephibyusingthescriptplot.tcljustasyoudidbefore(thereisadi erentcopyinthecurrentdirectory.)

TheresultisshowninFig.4.Plotthecenterofmassaswell,byopeningplot.tclandchangingthevarvariableto"Centerofmass".Thiscanbeaccomplishedbysimplycommentingthe rstsetvarline,anduncommentingtheother:

#setvar"atom1:phi"

setvar"Centerofmass"Angle of rotation

2

1.5

1

0.5

-0.5

0φ (rad)50010001500time (fs)200025003000

Figure4:Rotationangleplottedversustime.

8Weagainseearoughlyquadratictimedependenceatthebeginningofthetrajectorygivewaytoalinearone,againaconsequenceoftheLangevindamping.

9OpenthetrajectoryinVMD.WithVMDopen,gotothemaintclForcesFilesdirectory,thentypethefollowingintheTkConsole:

molloadpsfcommon/ubiquitin.psfdcdrot-a/rot-a.dcd

Challenge:Findthedependenceoftheterminallinearandangularveloci-tiesonthelangevinDampingparameterofthesimulation,setinthecon gura-tion le,aswellasthedependenceontheappliedforce.