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

[Justin A. Lemkul]

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.

-Justin

> SR
> 
> On Thu, Mar 25, 2010 at 5:17 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================