[gmx-users] walls and E-z

Dan Gil dan.gil9973 at gmail.com
Wed Nov 8 17:58:55 CET 2017

Hi Alex,

Is your system without walls periodic and continuous in all directions? I
can see a scenario where this sort of system will maintain charge
neutrality in the different reservoirs separated by the semi-porous
membrane. While cations will be transported, the charge in each reservoir
will be maintained constant because as one cation leaves, its periodic
image enters the same reservoir. It is a steady-state process.

In the system with walls, charge neutrality will be broken if cations are
transported across the membrane because it won't have a periodic image that
enters the same reservoir as it leaves. I think that the cation transport
would be more like capacitance since a constant electric field will only be
able to hold a finite number of cations across the membrane. This is an
equilibrium process.

Maybe try higher electric field?


On Fri, Nov 3, 2017 at 2:43 AM, Alex <nedomacho at gmail.com> wrote:

> Hi all,
> It appears that the external field is refusing to move the ions when walls
> are present. I am comparing two setups of a system that has an aqueous bath
> (1M KCl) split by a semi-porous (infinitely selective for cations) membrane
> in XY. The only difference between them is that one is periodic in XYZ and
> the other has two walls. The difference isn't minor -- consider K+ fluxes
> with and without walls: https://www.dropbox.com/s/jve0
> hqqpfkn4ui6/flux.jpg?dl=0
> Initially, ionic populations in each case are homogeneous. I realize that
> with walls the process will stop when all cations end up at the top of the
> box (and that's the goal). However, there is no flux right from the start.
> Relevant portion of the mdp with walls below (not sure if this is
> important, but 'ewald-geometry' directive isn't in the mdp without walls):
> pbc                 = xy
> nwall               = 2
> wall-type           = 12-6
> wall-r-linpot       = 0.25
> wall_atomtype       = opls_996 opls_996
> wall-ewald-zfac     = 3
> periodic_molecules  = yes
> ns_type             =  grid
> rlist               =  1.0
> coulombtype         =  pme
> ewald-geometry      =  3dc
> fourierspacing      =  0.135
> rcoulomb            =  1.0
> rvdw                =  1.0
> vdwtype             =  cut-off
> cutoff-scheme   = Verlet
> Any ideas?
> Thanks,
> Alex
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