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gromacs一些分析命令.pdf

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MolecularDynamicsHands-onSessionIITutorialonMDsimulationsusingGromacs3.3.3TsjerkA.WassenaarAnalysisofdatafrommoleculardynamicssimulationWhenthesimulationhasfinished,itistimetocontinuewiththeanalysisofthedata.Theanalysiscomprisesoftwostages.First,itisnecessarytoperformsomestandardcheckstoassessthequalityofthesimulations.Iftheresultsfromtheseanalysesshowthatthesimulationsarefine,thentheanalysesrequiredtoanswertheresearchquestionaskedcanbeperformed.Asasidenote,manyoftheanalysistoolsproducegraphsintheformof.xvgfiles.thesefilescanbeviewedwiththeprogramxmgrace,buttheycanalsobeviewedinaterminalusingthepythonscriptxvg2ascii.py.QualityassuranceThequalityassurance(QA)involvestestsfortheconvergenceofthermodynamicparameters,suchasthetemperature,thepressure,thepotentialandthekineticenergy.Convergenceisalsocheckedintermsofthestructure,throughtherootmeansquaredeviation(RMSD)againstthestartingstructureandtheaveragestructure.Nexttothat,ithastobecheckedthattherehavenotbeeninteractionsbetweenadjacentperiodicimages,assuchinteractionscouldleadtounphysicaleffects.AfinalQAtestinvolvesthecalculationoftherootmeansquarefluctuationsofatoms,whichcanbecomparedtocrystallographicb-factors.1ConvergenceofenergytermsWestartofwiththeextractionofsomethermodynamicparametersfromtheenergyfile.Thefollowingpropertieswillbeinvestigated:temperature,pressure,potentialenergy,kineticenergy,unitcellvolume,density,andtheboxdimensions.Energyanalysisisperformedwiththetoolg_energy.Thisprogramreadsintheenergyfile,whichisproducedduringthesimulation(1LW9-MD.edr).g_energywillaskforatermtoextractfromtheenergyfileandwillproduceagraphfromthat.Givethefollowingcommandtorung_energy:g_energy-f1LW9-MD.edr-otemperature.xvgThiswillgivealistoftheenergyandrelatedtermswhicharestoredinthe.edrenergyfile.Inourcase,thereare68termsintheenergyfile,eachofwhichmaybeextractedandgraphed.Thefirstnineentriescorrespondtodifferentenergytermsintheforcefield.Alsonotetheentriesfrom47onward,whichlistthetermssplitoverthegroupsProteinandNon-Protein,inc