[gmx-users] pbc on the "xy" direction

Berk Hess gmx3 at hotmail.com
Mon Mar 10 09:14:34 CET 2008

> To: gmx-users at gromacs.org
> Date: Mon, 10 Mar 2008 09:37:34 +0200
> Subject: [gmx-users] pbc on the "xy" direction
> Hi all,
> I am performing an air/water interface simulation and I want to implement anisotropic pbc condition (pbc on the "xy" direction) to my system. 
> I have searched the mailing-list but could not find an appropriate answer. In the manual, two options are given for -pbc ("xyz" and "no") .
> How can I implement it to my system? I use Gromacs 3.3.1 version.
> Thanks in advance
> Ozge Engin

This is a lot of work.
But luckily I have done this for version 4.0.
If you really need it you can check out the CVS version.

But in practice real 2D pbc is nearly never required.
One can use just as well use a box with a large z-dimension.
This is often also more efficient, since then one can still use grid neighbor searching,
which for large systems is MUCH faster than simple search.
Real 2D pbc is only required when one would for instance want
to evaporate molecules from a surface.


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