gmx rms -skip does not skip
Using the -skip option in gmx rms seems to have no effect. The output .xvg file with the RMSD values has all frames listed regardless. E.g. testing on the first 100 ps of a trajectory that has one frame per 1 ps, I get the same number of lines in the xvg output with these two commands
gmx rms -s topol.tpr -f traj_comp.xtc -fit rot+trans -e 100 -n index.ndx
gmx rms -s topol.tpr -f traj_comp.xtc -fit rot+trans -e 100 -skip 20 -n index.ndx
This is on Gromacs 2018.1. Haven't tested 2018.2 yet.