[gmx-users] Help about 2 D periodic boundary condition

David spoel at xray.bmc.uu.se
Mon Jan 13 19:00:09 CET 2003

On Mon, 2003-01-13 at 17:35, David L. Bostick wrote:
> Hello,
> For treatment of coulomb interaction in "slab geometry" i.e. the treatment
> of 3D systems with 2D periodicity there is a variable that can be set in
> the mdp file..
> ewald_geometry
> you can set ewald_geometry = 3d
> for a normal spherical ewald sum and
> ewald_geometry = 3dc
> for the addition of a correction term for slab geometry.
I recently looked into the code for this option. It only affects the
surface term, so if you set epsilon_surface = infinity there is no
difference. I assume that is the correct implementation (but haven't
read the paper), but I still have my doubts, since the PBC is computed
in three D just as usual. So I still would like to ask whether people
have tried this?  Is this really suitable for studying e.g. a vacuum

> > As for 2D PBC, it depends on what you want in the third direction.
> > You can for example make a two 'walls' of frozen atoms above and
> > below your system, or perhaps simply a vacuum boundary. The system
> > will still be treated in 3D PBC, but the third dimension will not
> > be relevant.
So what does it mean: not relevant? 

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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