[gmx-users] pbc = xy

Berk Hess gmx3 at hotmail.com
Wed May 4 16:25:24 CEST 2005

>From: Jennifer Rendell <rendell at cs.mun.ca>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] pbc = xy Date: Wed, 4 May 2005 11:18:58 -0230 (NDT)
>Dear Fellow Users,
>I am modelling a system of a lipid monolayer and water (on the headgroup
>side). I am considering ways to prevent the water from jumping, via
>periodic boundary conditions, over to the chain side of the layer.
>I have had no success using position restraints on a separately
>defined layer of water near that box side. The water molecules still pop
>over to the opposite side.

But if the system is periodic, it is periodic.
I mean that the water is already on the chain side, also if in the initial
structure the water is on top of the monolayer, via the periodic boundary
conditions it is also on the bottom.
You could have a layer of vacuum in between the water and the monolayer,
but that means you have a second (water-vacuum) interface.

>How difficult is it to modify the gromacs code to keep periodic boundary
>conditions in the x and y directions, but not have it in the z direction.

This is actually very simple for simple neighborsearching, you would only
need to remove the charge groups resetting in the z direction.
But simple search is very time consuming.
For the grid search it would not be easy as the number of cells in
the z direction is not limited.

Anyhow, such a solution would not help you as you would still have
the artificial (I assume you don't have this in experiment) water vacuum
interface and also water could evaporate and never return.


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