[gmx-users] GROMACS wall parameters

[shivangi nangia]

Thanks so much João, I will certainly try it.




On Tue, Jul 14, 2015 at 4:11 PM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> 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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