vmd教程 forces-tutorial

1TCLFORCES9

1.3Example2:Rotation

Wewillnowaddalayerofcomplexity:wewillforceatomsdi erentlybasedontheircoordinates.Inthisexample,wewillforceatomsinsuchawaythat,inadditiontoalinearforce,theproteinalsorotatesaboutanaxisparalleltothez-axisandthroughtheprotein’scenterofmass.

1Changetothedirectoryforces-tutorial-files/tclForcesFiles/rot-a.2LookattheNAMDcon guration le.Openthe lerot-a.namd.Attheend,weseethefollowing:

tclforces

setlinaccel

setangaccel

tclforcesscripton"3000"1rot-a.tcl

Thisisverysimilartothepreviousexample,buthereweprovideanadditionalscalartodescribetheangularacceleration.

3Nowlet’slookatthescriptitself.Openthe lerot-a.tcl.Theatomselectionpartatthebeginningisidenticaltothelastcase,sowewillnotrepeatthediscussion.Thenextpartofthe leisagainsimilar,butalsoprocessestheangularacceleration.

setlinaccel[vecscale[expr1.0/418.68]$linaccel]

setangaccel[expr$angaccel/418.68]

print"Linearacceleration:($linaccel)Ang*ps^-2"

print"Angularacceleration:(00$angaccel)Rad*ps^-2"

WeconverttoNAMDunits,justlikebefore.Thenweprintsomeinfor-mationaltextusingtheprintcommand.

4Nowwe’lllookatthecalcforcescommand.The rstpartisnearlythesameasinthepreviousexample.Thedi erencesarethechangeofoneoftheglobalvariables,andthefactthatwenolongerapplyforcesinthe rstloop.

proccalcforces{}{

globalatomsnumatomslinaccelangaccelnamd

loadcoordscoords

loadmassesmasses