[gmx-users] genion: can you place the ions at one location in the box?

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 30 01:20:20 CEST 2010

Justin A. Lemkul wrote:
> Smiruthi Ramasubramanian wrote:
>> Justin,
>> I tried to use an index file with atom numbers of the water molecules 
>> in the required volume.
>> But when I try to ionize the box, I get this error:
>> Fatal error:
>> The solvent group SOL is not continuous: index[717]=21689, 
>> index[718]=21696
>> This makes sense, but is there a way get around this?
> The fundamental requirement of genion is that the solvent is continuous 
> in the coordinate file.  If that's not true, genion won't work.  If you 
> have continuous solvent, a valid index group within that section should 
> work just fine.

Another option is to write your own script that replaces water molecules with 
the desired ion type; it should be relatively simple to randomly choose water 
molecules to replace based on simple coordinate criteria.  Updating the topology 
would have to be done manually, and you'd have to find a way to generate a 
syntactically correct coordinate file after making replacements, but that is 
also fairly simple I/O with, for example, Perl.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list