[gmx-users] RMSD command line doubt

[Neena Susan Eappen]

Hello gromacs users,

My goal is to calculate all-atom rmsd of every structure in the trajectory(.trr) to the final structure after simulation (.gro).

Q1) So, I don't understand the purpose of giving .tpr input file (which was the input structure file before production mdrun) as a structure file in the command.

        gmx rms -f peptide.trr -s peptide.tpr -o rmsd.xvg

Q2) When I use final structure .gro file (after production mdrun), I get the following warning:

Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files.

Please let me know if I am misunderstanding here anything.

Many thanks,
Neena