Never mind my previous question about using trjconv for fitting in
RMSD calculations. It does produce identical results compared to using
gmx rms alone. I just had a subtle error in atom numbering, which
resulted in bogus RMSD values.
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I ran into what seems to be a bug, namely that the -skip option in gmx
rms doesn't seem to do anything. The output always has the RMSD values
for all frames, even if -skip is specified. I filed a bug
(https://redmine.gromacs.org/issues/2565).
Then I resorted to trjconv to do the skipping
