[gmx-users] Non-periodic Boundary conditions

[Senthil Kandasamy]

Hi all,

I am a recent convert to GROMACS. I am wondering how one would
incorporate non-periodic boundary conditions in GROMACS. Specifically,
I am trying to simulate a membrane monolayer. I have a wall, with a
water layer on top of it with a lipid monolayer over that and nothing
(Air?? vacuum??) over the lipid monolayer. Assume periodic boundary in
the x and y directions.

Air
----
lipid
----
Water
-----
Wall.

How can I incorporate the wall into the picture ? I would have to
incorporate some sort of a uniform repulsive potential at the position
of the wall that would keep the water molecules from diffusing through
I guess .

Any ideas/suggestions?

Thanks. I am really enjoying learning GROMACS . It is indeed very
user-friendly. I hope to annoy you guys in the forthcoming months with a
lot of questions.


Senthil


The University of Michigan