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. > -- 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.