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? Read http://www.gromacs.org/Support/Mailing_Lists >>>>>>> >>>>>>> * For (un)subscribe requests visit >>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >>>>>>> or >>>>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>>>> >>>>>>> >>>>>>> -- >>>>> Gromacs Users mailing list >>>>> >>>>> * Please search the archive at http://www.gromacs.org/Support >>>>> /Mailing_Lists/GMX-Users_List before posting! >>>>> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>>> >>>>> * For (un)subscribe requests visit >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>>> send a mail to gmx-users-requ...@gromacs.org. >>>>> >>>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at http://www.gromacs.org/Support >>>> /Mailing_Lists/GMX-Users_List before posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to gmx-users-requ...@gromacs.org. >>>> >>>> >>> >>> > > -- > 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 > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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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