[gmx-users] adding walls? to EDL simulation?

Andreas adnad at gmx.net
Tue Sep 29 01:43:14 CEST 2015

hello users,

here is another and better phrasing of my problem. if i have a 3D pbc I 
create some sort of "dipol plate". And using only pbc=xy I can not use 
Ewald methods (PME) or pressure coupling (manual) without using two walls.

I don't understand the wall-atomtype variable? And how to use walls to 
fit my problem?

I just want to realize that the electrostatic force (or better all 
forces) of each graphene layer acts only in one z-direction and still 
use PME (or something for long range electrostatics) and pressure coupling.

I dont know if it is practical/possible to lower the distance for the 
PME, like a cut of distance and to define an empty room bigger then the 
actual experiment.

best regards


On 9/28/15 2:52 PM, ‪Andreas ‪ wrote:
> hello users,
> I have been building a small system with a graphene layer on each side 
> (Z-offset water and ions in between). i know which atoms in the top 
> file belongs two which layer and can easily add a charge. As i have 
> pbc conditions i would have in my current system both graphene layers 
> directly next to each other. should i simply make the box bigger, 
> after having added the solvent  (how to decide how big?) and create a 
> sort of empty space (does a big empty space effect the simulation 
> negatively?)  or can/should an pbc=xy be used with two walls, if so 
> how to setup those walls?
> best regards
> Andreas

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