[gmx-users] Dimer g_rms

[Carla Jamous]

Dear all,

I'm running my first simulation of a dimer.
When I run g_rms on Calpha (lsq fit and RMSD calculation on Calpha) to get
the RMSD of the whole dimer, the graph is ascending, till reaching a value
of 8 A.
in this case, I take a .tpr file, a .xtc file and a .ndx file of the whole
dimer.

However, when I run g_rmsd on Calpha, but this time, to get the RMSD of one
chain (one monomer), the graph is constant with value around 1 A. and this
for both chains, when taken alone.
In this case, I take a .tpr file, a .xtc file and a .ndx file of the
monomer.

So is this an error of using g_rms?

Thank you.

Carla
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