vmd教程 forces-tutorial(6)

vmd教程 forces-tutorial

1TCLFORCES

3First,weselecttheatomswe’reinterestedin:

setnumatoms1231

setatoms{}

for{seti1}{$i<=$numatoms}{incri}{

lappendatoms$i

}

foreachatom$atoms{

addatom$atom

}6

Thestructurewe’reusingisubiquitin,thesameproteinusedintheVMDandNAMDTutorials.Here,we’reusingtheproteinalone,invacuum,andsothestructurecontainsjust1231atoms.We rstbuildalistoftheatomicindices(NAMDatomindices,unlikeVMDatomindices,startat

1.)Foreachatom,wethencalltheaddatomcommand.ThistellsNAMDthatwewantaccesstothisatom’scoordinates.Forcesmaybeappliedtoanatomwithoutthiscall.

4Wenextconvertfromthenaturalaccelerationunits A·ps 2totheNAMDunitskcal/mol· A·amu,andprintsomeinformation:

setlinaccel[vecscale[expr1.0/418.68]$linaccel]

print"Linearaccelerationimparted:($linaccel)Ang*ps^-2"Notethattoprintmessagesfromtheforcescript,wemustusetheprintcommand,insteadoftheusualputs

command.NAMDUnits.The

basicNAMDunitsarekcal/molforenergy,

angstromsforlength,atomicmassunits(a.k.a.Daltons)formass,

andbarforpressure.Otherunitsarederivedfromthese,e.g.the

NAMDunitofforceis1kcal/mol· A≈69.48pN.Linearacceleration.LinearaccelerationisgovernedbyNewton’s

SecondLaw:

F=ma

Here,Fisaforcevector,misthemass,andaistheacceleration

vector.Thus,thisequationsaysthattoachieveaspeci edaccel-

eration,wemustapplyaforceequaltothataccelerationtimesthe

mass,inthesamedirectionwewanttoaccelerate.Inourcase,we

applyaforcetoeachindividualatom,scaledbyitsmasssothat

eachexperiencesthesameacceleration,andthustheproteinmoves

togetherasawhole.

5Theonlythingleftisthecalcforcescommand: