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

[David L. Bostick]

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.

For information on the usage of this correction term  see

J. Chem. Phys. 111(7):3155-3162

Good luck,
David

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Mon, 13 Jan 2003, Anton Feenstra wrote:

>
> > I am a newbie for GROMACS. Could you tell me if it is possible
> > to do 2 D periodic boundary condition for
> >        Coulomb interaction, and Brownian dynamics
> >        in the new version of GROMACS?
>
> IIRC, brownian dynamics was already possible for some time.
>
> 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.
>
>
> --
> Groetjes,
>
> Anton
>  ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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