[gmx-users] Calculate RMSD between snapshots of two trajectories

Dawid das addiw7 at googlemail.com
Mon Jul 31 12:53:23 CEST 2017

Dear Gromacs Users,

I would like to get a simple plot of RMSD versus time for two trajectories
in *.gro
format, where RMSD is calculated between structures at the same time, i.e.
snap11 - snap12
snap21 - snap22
snap31 - snap32
snap41 - snap42
where snap31 means third snapshot of the first trajectory. I have run
gmx rms   -s   npt-md2.tpr   -f   traj1.gro   -f2   traj2.gro   -n
index.ndx    -m    rmsd-small-superlarge.xpm

command and after converting the .xpm file to .eps I can see the
graphical representation of the matrix. However, I would rather see just
RMSD vs time plot as I explained above. How can I do it?

Best wishes,
Dawid Grabarek

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