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 <nedoma...@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 <sp...@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 <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 > >>>>>>> > >>>>>>> -- > >>>>>>> Gromacs Users mailing list > >>>>>>> > >>>>>>> * Please search the archive at http://www.gromacs.org/Support > >>>>>>> /Mailing_Lists/GMX-Users_List before posting! > >>>>>>> > >>>>>>> * Can't post? 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