vmd教程 forces-tutorial

2TCLBC202TclBC

InaNAMDcon guration le,onesetsupthesimulationparameters,suchasthetemperature,pressure,orauniformelectric eld,forthemolecularsystemasawhole.Inmanycases,though,youwillneedtoimposeboundaryconditions,applyanon-uniformelectric eld,orselectivelyapplyforcestoagroupofatomsofthegiventypeorlocatedinaparticulararea.Forthispurpose,youcanuseatclBC(whichstandsforTclBoundaryConditions)script.AtclBCscriptiswrittenintheTclprogramminglanguage,arudimentaryknowledgesofwhichwouldbeenoughformosttasks.Thescriptwillbeinterpretedline-by-line,thereforeslowingdownthesimulation,sometimesconsiderably.Forthisreasonyouwillwanttokeepyourscriptssimpleand

e cient.tclBCversustclForces.tclBCandtclForcesarebothscripting

interfacesthatallowtogetinformationabouttheatoms’positions

andapplyforcestoselectedatomsduringaNAMDsimulation.In

bothscripts,theforcecanbecalculatedindividuallyforeachatom,

dependingonitsuniqueIDnumberanditscurrentposition.The

maindi erencebetweentclBCandtclForcesisthatanindepen-

dentinstanceoftclBCisrunningoneachprocessor,andonlyatoms

formingthepatchtreatedbythatprocessorarevisibletothegiven

instanceoftclBC.ThisfeaturemakestclBCmoree cientthan

tclForces,whichisrunonjustoneCPU,butalsolimitsitsca-

pabilities.Ifyouneedtoapplyforcestoeachatomirrespectiveof

thepositionofotheratoms,usetclBC.Ontheotherhand,ifyou

havetoconsidermutualpositionsoftwoormoreatomsorgather

informationaboutthewholesystem,youwillneedtclForces.

ThewaythecoordinatesofatomsarewrappedaroundperiodicboundariesinatclBCscriptiscontrolledusingthecommandwrapmode,whichthatmayhaveoneofthefollowingarguments:

patchisthedefaultmode:theatom’scoordinatesareconsideredasthepositioninNAMD’sinternalpatchdatastructure.Thisisingeneraldi erentfromanatom’scoordinatesrelativetotheglobalorigin,sopatchmodeshouldnotbeusedunlessyouknowwhatyouaredoing.

Inmodeinput,theatom’scoordinatescorrespondtoitspositionintheinput lesofthesimulation.

Inmodecell,theatom’sequivalentpositionintheunitcellcenteredonthecellOriginisused.

Inmodenearest,theatom’sequivalentpositionnearesttothecellOriginisused.

Formostpurposes,modecellisagoodchoice.