[gmx-users] Help about 2 D periodic boundary condition
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:
> 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..
> 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?
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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