[gmx-users] walls and E-z
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?
> 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
>> 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
>> 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
>>> are present. I am comparing two setups of a system that has an aqueous
>>> (1M KCl) split by a semi-porous (infinitely selective for cations)
>>> in XY. The only difference between them is that one is periodic in XYZ
>>> the other has two walls. The difference isn't minor -- consider K+ fluxes
>>> with and without walls: https://www.dropbox.com/s/jve0
>>> 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
>>> box (and that's the goal). However, there is no flux right from the
>>> Relevant portion of the mdp with walls below (not sure if this is
>>> important, but 'ewald-geometry' directive isn't in the mdp without
>>> 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?
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