[gmx-users] question about g_rmsdist II

Erik Marklund erikm at xray.bmc.uu.se
Thu May 17 21:34:29 CEST 2007

17 maj 2007 kl. 15.49 skrev Mark Abraham:

> Fabrizio Mancinelli wrote:
>> Sorry, since I hadn't any answer to my question yet, I'm resending  
>> it to
>> give it visibility!
> If you don't get any luck, remember that the source code is  
> available for a reason :-)
>> ------- Messaggio inoltrato -------
>> Da: Fabrizio Mancinelli <fabrizio.mancinelli at unina2.it>
>> A: gmx-users at gromacs.org
>> Oggetto: question about g_rmsdist
>> Data: Mon, 14 May 2007 18:52:54 +0200
>> Dear all,
>> I would like to have some elucidation about g_rmsdist output.
>> Optionally, it outputs three matrices with the options -rms, -mean  
>> and -
>> scl. Questions are:
>> 1) Exploring .xpm files, I see there is a letter code which converts
>> color exa-codes to letters to values. The "resolution" is tunable  
>> with
>> option -nlevels, but the range is delimited by the highest calculated
>> value. Is there a way to assign a fixed range (in order, e.g., to
>> compare different trajectories of the same protein)?
> There was discussion on the list of implementing a way to write a  
> binary or ascii matrix. This would make it easy to do the kind of  
> comparison I think you want to do. Check the archives for the  
> resolution, but if there was one suitable for your needs, you'd  
> need to use the CVS version of this utility.
>> 2) -rms output, I guess, is the deviation from average distance, over
>> time, for each atom couple. I see my matrix is full of 0's. I  
>> expected
>> 0's on the principal diagonal (distance of an atom from itself is
>> obviously always zero), but others? It should mean atoms'  
>> distances RMSD
>> are 0, that is they do not deviate... but they don't look that  
>> fixed at
>> all from the trajectory! This is even more surprisingly in the -mean
>> output, which should contain, I guess, atom distances averaged over
>> time. In that case there are lots of 0's too. Maybe my "I guess" are
>> wrong...
> You've certainly got the wrong handle on -mean. Check the man page.
>> 3) What is, actually, -scl output?
I don't use g_rmsdist much, but the -h option tells me that  
"g_rmsdist can also produce matrices of the rms distances, rms distances
scaled with the mean distance and the mean distances and matrices  
with NMR
averaged distances (1/r^3 and 1/r^6 averaging).", which is a good clue.


> Don't know.
> Mark
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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