[gmx-users] walls and E-z

Dan Gil dan.gil9973 at gmail.com
Wed Nov 8 18:39:10 CET 2017


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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