[gmx-users] GROMACS wall parameters

[João Henriques]

You can do something else if you don't want to use position restraints on
the protein. You can try the "COM pulling" options, which can be used to
constraint the center of mass (COM) of two or more groups in a simulation.
In this case, you could add one for the COM of the protein and that of the
membrane. This is probably more a more elegant solution.

P.S.: I never done membrane simulations, so there may be better solutions
out there. Still, I don't think adding walls is good idea.

Best regards,
João

On Tue, Jul 14, 2015 at 8:54 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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