[gmx-users] walls and E-z
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 9 09:02:10 CET 2017
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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