[gmx-users] GROMACS wall parameters

[shivangi nangia]

Dear João,

Thanks for the reply.

The solution structures of the peptide certainly wont stay in the membrane.

The purpose of the study is to see if my peptide will go transmembrane.
Specifically, it is a 21 amino acid peptide that could potentially adopt a
transmembrane configuration in an oligomeric state like a bundle (perhaps
as trimer, tetramer, pentamer etc.) in POPC. The ultimate goal being to see
if peptide can create a pore in the membrane.

Since I could not find any protein-membrane docking software,  I want to
throw a few peptides in the membrane starting with transmembrane
orientation and see if they "find" each other while inserted in the
membrane. I want to constraint them from popping out of the membrane.

My peptide does contain a hydrophobic patch comparable to other
transmembrane peptides which gives me a certain confidence that it should
go transmembrane.

I am struggling to find a good starting point to set up such a system.

Thanks,
sxn




On Tue, Jul 14, 2015 at 2:54 PM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> 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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