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

[Ali Shomali]

Dear Philip

Thanks for your helpful advice

Actually, my simulation case is a slab of water that is covered by
monolayer in just one surface and the other surface is free and sometimes
some of water molecules (small number) escape from it. So is 3dc option
still applicable or I should return to original 3d method?
I appreciate your valuable suggestions.
Thanks

Ali


On Tue, Jun 20, 2017 at 6:50 PM, Philip Loche <ploche at physik.fu-berlin.de>
wrote:

> 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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