[gmx-users] walls and E-z

Alex nedomacho at gmail.com
Wed Nov 8 18:18:12 CET 2017

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 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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