[gmx-users] g_spatial

[Stella Nickerson]

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:

http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53492h-f4.gif

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
anything.

-Stella