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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
