[gmx-users] g_rms

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 3 15:01:59 CEST 2007

andrea carotti wrote:
> Hi,
>> 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 

If you read g_rms -h like I suggested last time, you'll see that -f2 and 
-s serve the same purpose with the former using a trajectory and the 
latter a single structure. That document doesn't say what happens when 
you use both... but the operation you're trying to do doesn't need both!

> Note that the pdbs (traj and ref) have the same number of atoms (same
> structure).
> 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.

There's an option to g_rms that writes a text matrix for importing into 
R. Look it up.


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