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

Smiruthi Ramasubramanian smiruthi at gmail.com
Tue Mar 30 01:05:33 CEST 2010


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?


On Thu, Mar 25, 2010 at 5:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Smiruthi Ramasubramanian wrote:
>> I am simulating an ion channel and require help placing a concentration of
>> ions at one side of the box (below the membrane).
> "Sidedness" is irrelevant in a periodic system; the water layers are
> continuous with PBC.
>  SETUP: membrane + embedded protein in the center of the cube.
>> I tried to generate a smaller cube (of the required volume below the
>> cube), solvate, add ions and then /cat/ with the *.gro file of my system
>> before solvating. But when I solvate the system with ions, the ions are
>> removed.
>> Any suggestions as to how to handle this problem?
> I don't fully understand what you tried to do, but it should be possible to
> solvate the unit cell normally, create an index group for the waters on one
> "side" of the membrane, and pass this index file to the -n flag of genion.
> Creating the index file may involve writing your own script to collect the
> atom numbers.  As far as I am aware, make_ndx cannot, for example, select
> all water molecules below/above some z-coordinate, which would be required
> for your situation.
> -Justin
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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