[gmx-users] walls and E-z

Alex nedomacho at gmail.com
Thu Nov 9 22:13:55 CET 2017 

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
>>>>>>>
>>>>>>> --
>>>>>>> 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-request at 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-request at 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-request at 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-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list