[gmx-users] g_densmap with Cartesian coordinates results in segvault, cylindrical does not

Vis, van der, J.S. j.s.van.der.vis at student.rug.nl
Thu May 18 11:16:08 CEST 2017

Dear all,

I am having some trouble with using g_densmap in the Cartesian coordinate
system. I want to calculate the density over a cylindrical pore, where the
z-direction is the axial direction. The sideview works just fine using:

g_densmap -f hyper.trr -s hyper.tpr -n hyper.ndx -od densmap.dat -amax 10
-rmax 15 -b 100000 -bin 0.05

and then defining the relevant index groups to get the right axial axis.
However, I also want to get a top-view of the pore, but this has less
success. No matter what I try, I get a segmentation fault. I know these are
hard to solve and that the problem is most likely somewhere in my
trajectory, but since the radial-axial calculation did work, I thought I
might have set some of the settings wrong. What I use is:

g_densmap -f hyper.trr -s hyper.tpr -n hyper.ndx -od densmap.dat -bin 0.05
-b 100000 -xmin -10 -xmax 10 -d1 300 -d2 300

I assume right now that the reference position for g_densmap is the center
of the coordinate system and that d1 and d2 is also centered. Can you see
something that I'm doing wrong? I would appreciate any help!

Thank you,

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