[gmx-users] genion: can you place the ions at one location in the box?
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 30 01:17:39 CEST 2010
Smiruthi Ramasubramanian wrote:
> 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=21689, index=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.
> 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
> 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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