[gmx-users] RMSD between two groups

[leila salimi]

Dear all,

I have a question regarding to analyse the trajectory that I have. I am
studying the interaction of peptide at interfaces, e.g Oxygen of
carboxylate group of side chains with Cations at the interface!
I would like to calculate the distance between Oxygen of carboxylate group
of side chains and specific ions of solid at the interface! I used gmx rms
but I think I did wrong calculation.

Could you suggest me which tool can give the overview of distance
fluctuation between two group of atoms?

Regards,
Leila