[gmx-users] question about g_rmsdist II

Fabrizio Mancinelli fabrizio.mancinelli at unina2.it
Thu May 17 14:45:34 CEST 2007

Sorry, since I hadn't any answer to my question yet, I'm resending it to
give it visibility!


------- 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)?

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

3) What is, actually, -scl output?

Thanks in advance to anybody who will answer.


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