[gmx-users] GROMACS wall parameters

[João Henriques]

You're most welcome. By the way, I found this old thread where Justin
suggests the same solution using the COM pulling:

http://comments.gmane.org/gmane.science.biology.gromacs.user/44479

This is probably your best option for "helping" the protein(s) to stay
inside the membrane. I would definitely toy with it a bit if I were you.

Good luck!

João

On Tue, Jul 14, 2015 at 9:56 PM, shivangi nangia <shivangi.nangia at gmail.com>
wrote:

> 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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