[gmx-users] Adding ions to membrane protein system

[João Martins]

As a completely pointless point since Mark just explained why it doesn't
make much sense to do it, you can achieve the same by separating your
waters in the [ molecules ] directive, calling each whatever group name you
define on your index file. Then you can use genion for each subset of
waters, which will only replace waters within each of the molecule subsets
you defined.

@Mark

Would this be possible with pbc = xy and nwall = 2? I'm quite sure
energetically it wouldn't make much sense, but I think it would indeed
succeed on keeping the ions in the correct membrane side.

Best regards,
João Martins



*Joao Martins*

joaomartins139 at gmail.com

On Thu, Jul 2, 2015 at 11:01 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> 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.
>
> Mark
>
> 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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