[gmx-users] how to change the color scale on covariance matrix plots made with g_covar ?

Evelyne Deplazes e.deplazes at uq.edu.au
Thu Nov 3 07:25:29 CET 2016

Hi guys

I am using g_covar to calculate the covariance matrix for 3 different
simulations systems. The commands I use are

echo "21 17" | ~/programs/gromacs/3.3.3/bin/g_covar -f
trajout_channel_allwindows.xtc  -s run_1.tpr -n index.ndx -o
eigenval_chABC_fitwithoutthumb_allwindows.xvg -l
covar_chABC_fitwithoutthumb_allwindows.log -xpma

xpm2ps -f covar_chABC_fitwithoutthumb_allwindows.xpm -o

I then repeat the same thing for the two other systems so I end up with 3
.xpm and .eps files. The Problem is that the color range of the matrices.
They a) don't range from -X to +X (eg for one of them matrices it goes
from -1.2 to 2.92) and b) the range is different for each matrix. That
makes it very hard to compare them

How can I set the scale for the matrix either in g_covar? Or do have to
post-process the .xpm file? If so, how?


Dr. Evelyne Deplazes, PhD
NHMRC Early Career Fellow (Curtin University)
Visiting Academic, The University of Queensland
St. Lucia, QLD 4072, Australia

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