[gmx-users] GROMACS wall parameters

[João Henriques]

Dear Shivangi,

To me - if I understood your problem correctly - there's no point in using
walls. Why don't you just use position restraints for the protein? When I
think of walls, I think of surface adsorption studies and such.
Furthermore, when you use walls in gromacs you're including an additional
protein-surface LJ term to the system Hamiltonian, which is something you
definitely don't want in this case, since you just want to use them as
"inert barriers".

One more thing: I don't know what system you're working on and what's your
purpose, but if the protein isn't stable inside the membrane, then that
probably means that there's a bunch of other issues to consider first,
before trying ad-hoc approaches.

Best regards,
João


On Tue, Jul 14, 2015 at 6:19 PM, shivangi nangia <shivangi.nangia at gmail.com>
wrote:

> Hello All,
>
> Is there any tutorial/example of how to apply wall potential in GROMACS.
>
> I basically want to design a system where there are two walls just above
> and below the head groups of a bilayer, so that I am able to restrain an
> inserted peptide from popping out to the surface or in water.
>
> http://manual.gromacs.org/online/mdp_opt.html#walls
>
>
> Thi link says:
>
> a) I can apply 2 walls, one being at z=0 and the other at z=z-box
>
> here "box" means the length of the box in z-direction?
>
> b) *wall-atomtype:*
> the atom type name in the force field for each wall. By (for example)
> defining a special wall atom type in the topology with its own combination
> rules, this allows for independent tuning of the interaction of each
> atomtype with the walls.
> Is there a way that I can specify that the "head-groups" in the .itp file
> as wall-atomtype?
>
> Kindly guide.
>
> Thanks,sxn
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