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 <nedoma...@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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