vmd教程 forces-tutorial

1TCLFORCES

foreachatom$atomsmass$masses{

setlinforce[vecscale$mass$linaccelnamd]

setr[vecsub$coords($atom)$com]

setx[lindex$r0]

sety[lindex$r1]

setrho[exprsqrt($x*$x+$y*$y)]

setphi[expratan2($y,$x)+$MPI/2]

if{$atom==1}{

print"atom$atom:

}phi=$phi"16

setangdir"[exprcos($phi)][exprsin($phi)]0.0"

setangmag[expr$angaccel*$rho*$mass]

setangforce[vecscale$angmag$angdir]

setforce[vecadd$linforce$angforce]

addforce$atom$force

}

}

13Nowrunthesimulation,justasyouhaveinpreviousexamples:

namd2rot-b-short.namd>rot-b-short.log

Ifyouhaveaccesstoacluster,runitonthecluster—refertolocalin-structionsforhowthisisdone.Thissimulationwillrunforjust100steps,sothatthebenchmarktimesareprinted.Inthenextsection,wewillseehowtoimprovethisperformance.

Ifyouareinterested,examinethe lesrot-b-long.logandrot-b-long.dcdintheexample-outputdirectory,whichwereproducedwithaslightlylongersimulation.WhenloadingthetrajectoryinVMD,usethePSFcommon/ubiquitinsolvate.psf

1.5Example4:ImprovingE ciency

Inmostcases,it’sunnecessarytorecalculatetheforcevaluesappliedateachtimestep.Dependingonthesituation,onemaybeabletorecalculateevery1000steps,savingalotofcomputationale ortandthereforeincreasingthespeedofthesimulation.Inthissection,wewillseehowtodothat.

1Changetothedirectoryforces-tutorial-files/tclForcesFiles/rot-c.2OpentheNAMDcon guration le,rot-c-short.namd.Thenewlinethistimeis

setforcesRecalcFreq10

Asitsnameimplies,thisparametersetshowoftenourforceswillberecalculated.