On 08/11/17 22:29, Alex wrote:
Okay, same thing with 0.5V/nm. I think it's fairly safe to say that there's
something wrong here...
Haven't followed but if a bug is suspected please file a report at
redmine.gromacs.org.
Alex
On Wed, Nov 8, 2017 at 12:25 PM, Alex <nedoma...@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.gil9...@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 <nedoma...@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 <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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