vmd教程 forces-tutorial(19)

发布时间：2021-06-05 来源：未知

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vmd教程 forces-tutorial

1TCLFORCES

8Nowrunthesimulation:

namd2rot-c-short.namd>rot-c-short.log19

Again,thisisashortsimulation,running100steps,parethespeedofthissimulationtothelast.Thereshouldbeasigni cantdi erence—comparingtheexample lesrot-b-short.logandrot-c-short.log,whichwererunonjustasingleCPU,thereisnearlya15%speedincrease.AsthesizeofthesystemandthenumberofCPUsincrease,applyingtclForcesef- cientlybecomesevenmoreimportant:comparingrot-c-long.logwithrot-b-long.log,bothrunon20processors,rot-cisalmost60%faster!

Onceagain,therearesampleoutput les,rot-c-long.dcdandrot-c-long.logintheexample-outputdirectory,andshouldagainbeloadedtogetherwiththePSF lecommon/ubiquitinsolvate.psf.

Challenge:Taketheprovided lekcsa,andusethepartialstructurekcsaasatargettoopenthechannelusingtclForces.YounowknowthebasicsoftclForces.Inthenextsection,youwilllearnaboutasimilarfeatureofNAMDcalledtclBC,whichissuitablefordi erentcircumstances.

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