Re: [gmx-users] walls and E-z

[Alex]

I'll just reply here, since I seem to be unable to respond to Berk's 
message on redmine.


On Fri, Nov 10, 2017 at 1:12 AM, > wrote:
Issue #2291  has 
been updated by Berk Hess.



  * *Status* changed from /New/ to /Rejected/

This is likely not a bug. The wall and electric field code are 
completely independent.
I guess that what you are seeing is the effect of the ewald-geometry. 
Using geometry=3DC heavily penalizes the build-up of a dipole, so 
alignment of molecules with the electric field decreases by a factor 
about equal to dielectric constant. You can verify this by changing to 
3D Ewald geometry.
What Ewald boundary condition you actually want depends on what you 
want to do. This is a critical aspect and you need to think this 
through well.


I tried with the default setting for ewald-geometry, which is 3d -- *no 
difference* and no ion flux to speak of. My basic solution right now is 
to introduce an actual atomistic wall while keeping full PBC and not 
using Gromacs implementation of walls. My setup is incredibly simple, as 
I am trying to polarize an ionic solution along the Z-axis.


Alex


On 11/9/2017 3:16 PM, Alex wrote:
Got it --  filed on redmine. With a "real" wall and E-z = 0.1V/nm, 
only five ions cross, which can be confirmed by simple calculations as 
sufficient to counteract the external field, given the membrane's own 
crossing barrier.


Alex

On Thu, Nov 9, 2017 at 2:21 PM, Dan Gil > wrote:


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 > 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

> >
> 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 > 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
>
> 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 > 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
> >>
  

Re: [gmx-users] walls and E-z

[Alex]

Got it --  filed on redmine. With a "real" wall and E-z = 0.1V/nm, only
five ions cross, which can be confirmed by simple calculations as
sufficient to counteract the external field, given the membrane's own
crossing barrier.

Alex

On Thu, Nov 9, 2017 at 2:21 PM, Dan Gil  wrote:

> 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  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  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 
> > 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  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  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+
> > 

Re: [gmx-users] walls and E-z

[Dan Gil]

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  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  >
> 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  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 
> 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  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  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):
> 

Re: [gmx-users] walls and E-z

[Alex]

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 
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  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  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  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  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 

Re: [gmx-users] walls and E-z

[David van der Spoel]

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  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  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  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  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 & 

Re: [gmx-users] walls and E-z

[Alex]

Okay, same thing with 0.5V/nm. I think it's fairly safe to say that there's
something wrong here...

Alex

On Wed, Nov 8, 2017 at 12:25 PM, Alex  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  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  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  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
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>> > * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] walls and E-z

[Alex]

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  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  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  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
> >
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> > 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 

Re: [gmx-users] walls and E-z

[Dan Gil]

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  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  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
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] walls and E-z

[Alex]

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  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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