[gmx-users] g_rms

andrea carotti andcar at chimfarm.unipg.it
Wed Oct 3 14:32:06 CEST 2007

> You should be getting such a 2200x33 matrix. My guess is that the 
> command line or files that you're using are not what you think they
> are :-)
my command line is 

g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 

Note that the pdbs (traj and ref) have the same number of atoms (same
During the calculation i can see that it is creating the 2200x33 matrix,
but on the rmsd.xvg i find only two columns. From the xpm and dat files
i can't extract the matrix (i don't know) to a text file.
I hope this could clarify better my question

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