[gmx-users] Adding ions to membrane protein system

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 2 23:01:22 CEST 2015


Your membrane is probably in the x-y plane, so you just insert ions
everywhere and delete from the .gro file all that have a z coordinate
bigger than whatever value aligns with the bottom of your membrane, and
correct the number of atoms in the .gro and .top file accordingly.

This won't help you because you only have a single chunk of water, so your
concentration differential will just diffuse away. You could use
flat-bottomed position restraints in GROMACS 5 to help with that, perhaps.
Or the Computational Electrophysiology feature.


On Thu, Jul 2, 2015 at 7:37 PM anu chandra <anu80125 at gmail.com> wrote:

> Dear Gromacs users,
> I am working with membrane proteins. I have build my membrane-protein
> systems  with a layer of water bed on top and bottom of the membrane. Now,
> I would like to add a specific  concentration of KCl to bottom layer of the
> water bed. Can anybody suggest me a way to add ions to a specific water
> layer of the membrane-protein system?
> Thanks in advance
> Anu
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