[gmx-users] Spacial density map
Dallas.Warren at monash.edu
Fri Oct 31 00:46:41 CET 2014
If you have access to 4.0.7 then you can do it, that will generate the SDF based on multiple molecules. Unfortunately, that functionality has been removed from the script in versions after that.
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> Stella Nickerson
> Sent: Friday, 31 October 2014 10:08 AM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Spacial density map
> I am simulating an ionic liquid, and I want to generate a spatial
> map on the anion around the cation. I want an image that looks like
> That is, I want the isosurface of the cation right around one anion.
> 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
> box (a big white cloud. Not useful).
> First I ran:
> trjconv -s md.tpr -f mdDone.trr -o noPBC.trr -pbc mol -ur compact -
> with the cation as the group to be centered and the entire system as
> 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
> index group and used that as the solute. That didn't seem to change
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