vmd教程 forces-tutorial

2TCLBC21

2.1Example1:MakingaBubble

Imaginethatyouhaveawaterbox,andyouwanttocreateasphericalbubbleofvacuum.Youcandothatbyapplyingforcestoeveryatomfoundinsidethisspheretopushitout.Toavoidinstability,youwouldwanttostartwithasmallbubbleandthenincreaseituntilthedesiredsizeisreached.Therateofincreasingthesizeofthebubbleisuptoyou.Ifthisrateistoolarge,someatomswillbepushedtoohardandthereforemovetoofast,causingthesimulationtocrush.Fast-movingatomsmayalsobreakthestructureofadouble-strandedDNAoranothermolecularcomplexheldtogetherbyrelativelyweaknon-bondedinteractions(vanderWaalsandelectrostaticforces).Evenifthesimulationremainsstable,youshouldwatchthechangesintemperatureandpressuretomakesurethattheenergyin ux,whichisequaltotheworkdonebytheforceyouareapplying,hasenoughtimeto

dissipate.Choosingtheloadingrate.Generallyyouwouldwanttokeep

theperturbationofthesystemaslowaspossiblebyimposingany

externalforcesasslowlyasyoucana ordgivenyouravailablecom-

putationalresources.Itisagoodidea,though,torunatrialsim-

ulationatafastpacetoseewhatishappeningtothesystem,and

therebygetanideaofhowfastyoucanmovethingswithoutlos-

ingthestabilityofthesimulationorincreasingthetemperatureor

pressurebeyondreason.

1Openthe letclBCfiles/BUBBLE/eq04.bubble.namdinatexteditor.Scrolldowntotheendofthe letothelinetclBCon.

Youshould ndthefollowingcode:

tclBCon

tclBCScript{

setbubbleCenter"0.00.00.0"

settclBCScriptbubble.tcl

source$tclBCScript

}

tclBCArgs{0.15.0.015.}

SinceatclBCscriptiscalledfromNAMD,itisreferencedNAMDcon- guration le,whichisalsoagoodplacetosetthescriptparameters.TheNAMDcommandtclBConturnstheTclBCinterfaceon.Inourexample,tclBCScript{...}containstheinitializationofakeyvariableandareferencetothe lethatcontainsthescriptitself:source$tclBCScript.Ifthescriptisshort,itcanbeplacedentirelywithinthebodyofthecommandtclBCScriptintheNAMDcon guration le.Finally,thecommandtclBCArgsisusedtopassalistofvariablestothemainTclBCprocedurecalcforces(wewilltalkaboutitverysoon).Inthiscase,thefourargumentsfoundincurlybracketshavethemeaning:“makeabubblestartingfromradius0 Aandincreaseitto15 Aata rateof0.01Apersimulationstep,byapplyingforcesof5kcal/mol·A.”