[gmx-users] g_spatial

Stella Nickerson stella.nickerson at gmail.com
Thu Oct 30 23:47:23 CET 2014

I am simulating an ionic liquid, and I want to generate a spatial density
map on the anion around the cation. I want an image that looks like this:


That is, I want the isosurface of the cation right around one anion. The
people who made that image say they used VMD, but I can't figure out how to
do it. I try to use g_spatial, but I get a density map every anion in the
box (a big white cloud. Not useful).

First I ran:

trjconv -s md.tpr -f mdDone.trr -o noPBC.trr -pbc mol -ur compact -center
with the cation as the group to be centered and the entire system as the
output group.

Then I ran:

trjconv -s md.tpr -f noPBC.trr -o fit.trr -fit rot+trans

Then I ran:

g_spatial -f fit.trr -s md.tpr -nab 20

(nab 20 because -nab 10 resulted in a sigmentation fault.)

I also tried making an index file defining exactly one cation as it's own
index group and used that as the solute. That didn't seem to change


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