[gmx-users] g_densmap: adsorbed species and output format

anouri a.nouri at gmail.com
Wed Dec 12 03:20:24 CET 2012

Dear Gromacs users,

I am writing to ask about g_densmap command:

If there are species adsorbed (stagnant) or structured around a frozen
group, for which I want to obtain the density distribution map, g_densmap
calculates unrealistically high densities. (like 2000 /nm3 of water...). 
So in visualization, the regions with descent density (like ~ 30 /nm3 for
bulk water) will be shown with the same color code as zero density (because
.xpm supports only 16 colors). I was wondering if there was a way to obtain
the numerical density values (in a 2d matrix) as the output of g_densmap,
rather than the .xpm format.

(One solution is to impose the maximum with an educated guess for -dmax
option, but having the actual numbers would be nicer.)

Furthermore, I was wondering if there is readily a code available to convert
the .xpm image to a matrix with numerical values, if I want to do a
calculation on the density map. Currently I convert the .xpm file to .png,
then import it to MATLAB and use the image processing toolbox to analyze. I
believe this introduces some error to the calculation.

I look forward to receiving your advice!
Thank you,


Amin Nouri
MSc student
Chemistry department, Simon Fraser University

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