[gmx-users] RMSD value

[Fitsiou, Eleni]

Dear users,

I have a question regarding the calculation of RMSD value for a big system comprising of many replicas of the same peptide.
I know that with RMSD fit you can choose to “superimpose” your reference structure to the one from the trajectory (rot+trans). My question is when supplying gmx rms with -s the structure file (that has all the peptides) does it treat it as a whole object? should I supply with the s flag an em.tpr of a single peptide (and ignore the warning about mismatch of number of atoms?).
I am getting big values (nm) and trying to understand what I did wrong. I would like gmx rms to give the average value for displacement for all the peptides for each frame from the trajectory. 

Thank you in advance!

Best, Eleni