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

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 25 23:17:50 CET 2010

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


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