Rg is a polymer statistic, related to the compactness of a folded polymer, and most meaningful for a polymer chain that folds into a roughly spherical shape.
CHARMM has several tools for looking at relative motions of residues, such as COOR COVAriance and COOR PAXA (corman.doc). I believe some of the fluctuation based time series in CORREL (correl.doc) can also be useful for evaluating relative motion vectors.
Also, normal mode calculations and quasiharmonic analysis (vibran.doc) might provide some insight into "hot" residues.
For distances, the DISTance time series works fairly well for a single pair of atoms, one from each residue.
Last edited by rmv; 12/03/09 08:49 PM.