[gmx-users] a problem about ewald geometry=3dc

[Philip Loche]

Dear Ali,

to use the 2D correction you only have to make sure that your box height is at least 3 times larger than your slab. This does not depend on the explicit position of your slab. So pbc=xyz does not make any problems, if your atoms always “stay” in a thin slab and do not move around in the whole box! The whole technique is explained in this paper: http://dx.doi.org/10.1063/1.479595

Best

Philip


—

Philip Loche
Department of Physics
Freie Universität Berlin
Arnimallee 14, Room 0.3.30
14195 Berlin, Germany

phone: +49 (0)30/838-55279

> On 19. Jun 2017, at 21:37, Ali Shomali <ali.shomali111 at gmail.com> wrote:
> 
> Hello to all Dear Gromacs Users
> 
> I'm modeling a lipid monolayer with vacuum space on top of it and with
> periodic boundary conditions in xyz directions. the vacuum space is about
> 10nm to minimize any possible effect of periodicity. for using ewald
> summation as manual mentions :
> 
> *"The geometry to use for Ewald summations. 3d means the sum is performed
> in all three dimensions. If your system has a slab geometry in the x-y
> plane you can try to increase box z dimension and use the 3dc geometry. The
> reciprocal sum is still performed in 3d, but a force and potential
> correction applied in the z dimension to produce a pseudo-2d summation. In
> the future there might also be a true2d option, but this is not working y"*
> 
> 
> however it causes warning :
> 
> With PME and ewald_geometry = 3dc you should use pbc = xy
> 
> since I can't use pbc=xy , can I use 3dc with pbc in xyz and ignore the
> warning ? how this affect results?
> 
> Thanks for your time and attention
> Ali
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