[gmx-users] walls and E-z

[Alex]

Good question. Dielectric breakdown of water is generally poorly understood
and the threshold depends on the ionic strength, but 0.4-0.5V/nm is
generally where the fun begins. MD modelers working with solvated systems
casually ignore this, unless they have the great misfortune of getting me
as a reviewer. :)
That aside, I believe your suggestion is sound, at least to see if what I
observe is an outright bug.

Thanks,

Alex

On Wed, Nov 8, 2017 at 10:39 AM, Dan Gil <dan.gil9973 at gmail.com> wrote:

> Yes I saw your plot and it is simply around 0 with walls.
>
> What is the field required for dielectric breakdown?
>
> On Wed, Nov 8, 2017 at 12:18 PM, Alex <nedomacho at gmail.com> wrote:
>
> > Hi Dan,
> >
> > Yup, periodic, continuous, and electrically neutral. I suggested a
> similar
> > thought in my question, i.e. with walls any transport would definitely be
> > transient and self-limited. However, nothing is transported even in the
> > perturbative sense, as you can see from the flux. The behavior is that
> of a
> > system without any driving field.
> >
> > The electric field is already quite high (0.1 V/nm) and of course I could
> > go completely nuts and exceed the experimental dielectric breakdown
> > threshold values for water, but the question remains, no?
> >
> > Thanks,
> >
> > Alex
> >
> >
> >
> > On 11/8/2017 9:58 AM, Dan Gil wrote:
> >
> >> 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?
> >>
> >> Dan
> >>
> >> 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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