In this chapter different ways of analyzing your trajectory aredescribed. The names of the corresponding analysis programs are given.Specific information on the in- and output of these programs can befound in the tool documentation here.The output files are oftenproduced as finished Grace/Xmgr graphs.
First, in sec.聽Using Groups, the group concept in analysis isexplained. Selections explains a newer concept of dynamicselections, which is currently supported by a few tools. Then, thedifferent analysis tools are presented.
Using GroupsDefault GroupsSelectionsLooking at your trajectoryGeneral propertiesRadial distribution functionsCorrelation functionsTheory of correlation functionsUsing FFT for computation of the ACFSpecial forms of the ACFSome ApplicationsCurve fitting in GROMACSSum of exponential functionsError estimationInterphase boundary demarcationTransverse current autocorrelation functionViscosity estimation from pressure autocorrelation functionMean Square DisplacementBonds/distances, angles and dihedralsRadius of gyration and distancesRoot mean square deviations in structureCovariance analysisDihedral principal component analysisHydrogen bondsProtein-related itemsInterface-related items