[gmx-users] walls and E-z

[Alex]

Okay, same thing with 0.5V/nm. I think it's fairly safe to say that there's
something wrong here...

Alex

On Wed, Nov 8, 2017 at 12:25 PM, Alex <nedomacho at gmail.com> wrote:

> 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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