[gmx-users] walls and E-z
Dan Gil
dan.gil9973 at gmail.com
Thu Nov 9 22:21:50 CET 2017
I simulated ionic liquids with walls and electric field. The field was
processed in my case.
On Thu, Nov 9, 2017 at 4:13 PM, Alex <nedomacho at gmail.com> wrote:
> David, not sure this is a bug. For the moment, can someone simply tell me
> if external field directive is processed when walls are used?
> I fixed the issue by introducing an actual wall as part of the system and I
> think this behavior may be by design. I mean, why apply driving fields when
> the system is impermeable?
>
> Alex
>
> On Thu, Nov 9, 2017 at 12:03 AM, David van der Spoel <spoel at xray.bmc.uu.se
> >
> wrote:
>
> > 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 <nedomacho at 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.gil9973 at 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 <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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> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Head of Department, Cell & Molecular Biology, Uppsala University.
> > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> > http://www.icm.uu.se
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