[gmx-users] Spacial density map

[andrea spitaleri]

Hi,

You could try to use in vmd VolMap tool in order to generate the dx 
isosurface.

hope it helps

and

On 31/10/2014 00:46, Dallas Warren wrote:
> 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.
>
> Catch ya,
>
> 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
>> 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.FreeConte
>> nt.ImageService.svc/ImageService/Articleimage/2013/CP/c3cp53492h/c3cp53
>> 492h-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.
>> --
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-- 
Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557