[gmx-users] GROMACS wall parameters

[shivangi nangia]

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