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
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