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 before using gmx rms,
and figured I might as well do the fitting of the structures at that
stage, since it has the added benefit of calculating the fit just
once. I need RMSD values for different parts of a protein, but using
the same fit to the reference structure. To my surprise, the RMSD
values are different when the frames are fitted with trjconv and then
calculated with gmx rms -fit none, as compared to just using gmx rms
with -fit rot+trans. In my case, when using the protein backbone for
both the fit and the RMSD calculation, the RMSD values are roughly 0.5
Å larger for the trjconv-fitted trajectory, but it's not an exact
systematic shift.
Am I missing something obvious here? Are these two procedures supposed
to do the same thing or not?
gmx rms alone:
gmx rms -s topol.tpr -f traj_comp.xtc -fit rot+trans -skip 100 -n index.ndx
(-skip does not work; select protein backbone for fit and for RMSD)
trjconv + gmx rms:
gmx trjconv -f traj_comp.xtc -s topol.tpr -fit rot+trans -skip 100
-n index.ndx
(select protein backbone for fit)
gmx rms -s topol.tpr -f trajout.xtc -fit none -n index.ndx
(select protein backbone for RMSD calculation)
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