[gmx-users] g_rms matrix between wt and mutant

Shay Teaching shay.teaching at gmail.com
Mon Sep 12 16:27:01 CEST 2011

Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory
and one mutant trajectory using the following command:

g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n

The file wt_backbone.ndx contains the backbone of the protein (Backbone
indices are identical between wt and mutant).

The result is that I am getting a well deserved error saying that wt.xtc and
mutant.xtc has different number of atoms (the tpr itself):
Fatal error:
Second trajectory (76128 atoms) does not match the first one (76129 atoms)

So the question becomes: Is there a (convenient) way to produce rms-matrix
between wt and mutant?
Or perhaps circumvent this problem in some other way?
I tried looking into g_confrms, but apparently it works only on two frames
instead of trajectories.

Thanks a lot,
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