[gmx-users] Adding ions to membrane protein system

[Mark Abraham]

Hi,

Dunno, never tried the walls code.

Mark

On Thu, Jul 2, 2015 at 11:37 PM João Martins <joaomartins139 at gmail.com>
wrote:

> 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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