vmd教程 forces-tutorial

1TCLFORCES

proccalcforces{}{

globalatomsnumatomslinaccelloadcoordscoords

loadmassesmasses

setcomsum"0.00.00.0"

settotalmass0.0

foreachatom$atoms{

setforce[vecscale$masses($atom)$linaccelnamd]

addforce$atom$force

settmp[vecscale$masses($atom)$coords($atom)]

setcomsum[vecadd$comsum$tmp]

}

setinvmass[expr1.0/$totalmass]

print"Centerofmass=[vecscale$invmass$comsum]"

}7

Thescriptstartswiththeglobalcommand,whichimportsthevariablesnamedsothattheycanbeaccessedinthecalcforcescommand.

Nextwecallthecommandloadcoords.ThissetsthevariablecoordstoaTclarrayofcoordinatesoftheatomsthathavebeenaddedusingaddatom.Inthiscase,ofcourse,thatisalltheatomsofthesystem.ArrayelementsinTclareaccessedusingparentheses.Similarly,loadmassesretrievestheatomicmasses,puttingtheminanarraynamedmasses.

Thenweloopthroughtheatoms,applyingthespeci edforcetoeachusingtheaddforcecommand.Alongtheway,wealsocalculatethecenterofmassoftheprotein.WeseetwomoreTclcommandsinactionshere:vecaddandvecscale.Theseaddtwovectorsandmultiplyavectorbyascalar,respectively.

6Becausethesystemissosmall,youcanrunitonyourdesktoporlaptopwithouttrouble,andseetheproteinmove.Runthe lepush.namd.Withanormalinstallation,youwoulddothiswiththecommand

namd2push.namd>

push.logCoordinates.CoordinatesintclForcesarenotwrappedaround

theunitcell.Ifyouneedwrappedcoordinatesforwhateverreason,

youmustwrapthemyourselfusingtheperiodiccelldimensionsand

origin.

7Afterthis nishes,wewanttoseehowtheproteinwasa ected.WewillnowuseVMD’sMultiPlotplugintoviewtheresults.Openthe leplot.tclinyourfavoritetexteditor,andchangethe rstlinetobethelocationofthelog leyoujustcreated,e.g.

setlogpush.log

ifyounamedthelog lepush.log.Torunthescript,eithertype