vmd教程 forces-tutorial

1TCLFORCES51TclForces

Inthisunit,youwilllearnaboutNAMD’sTclForcesfunctionality.AlthoughmanyuserneedswereanticipatedinthedevelopmentofNAMD,toanticipatethemallspeci callywouldbeimpossible.TclForcesallowsuserstoeasilysup-plementthebuilt-inconstraintandforcefunctionalitywithscript-basedforces.

1.1Introduction

ThebasicideaoftclForcesissimple:weprovideNAMDwithaTclscriptwhichtellsNAMDtoapplycertainforcestocertainatoms.Theonlyspecialrequirementofthisscriptisthatitde neacommandnamedcalcforces.ThiscommandiscalledbyNAMDeachtimestep.Withinthescript,wecanaccessatomicIDs,positionsandmasses.Inthisunit,wewillseehowtousetclForcesthroughfourexamplesofincreasingcomplexity.

1.2Example1:ConstantForces

Forour rstexposuretotclForces,wewilldosomethingverysimple:applyaconstantnetforcetoasystem.

1First,let’slookattheNAMDcon guration le.Gotothedirectoryforces-tutorial-files/tclForcesFiles/pushandopenthe lepush.namd.Everythingisstandardaboutituntiltheend,whereweseesomeunfa-miliarlines:

tclforceson

setlinaccel"3000"

tclforcesscriptpush.tcl

The rstlinesimplyturnstclForceson.Thesecondsetsaparameterfortheaccelerationthatwe’lluseinthescript,aswe’llsoonsee.Thelastlineisthenameofthescriptwhichactuallydoesthe

work.In-linescripts.Itisalsopossibletoincludethecontentsofyour

tclForcesscriptdirectlyinyourNAMDcon guration le.Instead

ofprovidingthenameofascript,wecouldinsteadwritethescript

contentswithincurlybraces:

tclforcesscript{

...contentsofscript...

}

Thisismostusefulforparticularlyshortscripts.

2Nowlet’slookatthescript.Openthe lepush.tcl,inthesamedirectory.