[gmx-users] gmx potential

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 2 17:40:40 CEST 2018 

Hi,

Shouldn't you be comparing the distribution with and without the external
field to verify that it has an effect that is physically consistent? Even
if there was output from mdrun that said "the applied field was blah blah
on step x" that still wouldn't mean anything unless the other output is
consistent.

Mark

On Mon, Apr 2, 2018, 15:01 Shreyas Kaptan <shreyaskaptan at gmail.com> wrote:

> Hi.
>
> Can anyone else try to answer my query about using gmx potential? I feel
> there must be a way to use it to check the potential as applied by external
> electric field.
>
> Shreyas
>
> On Thu, Mar 22, 2018 at 5:08 PM, Alex <nedomacho at gmail.com> wrote:
>
> > Not sure what you mean by "correct." The "voltage" would be the field,
> > times the box size in the direction of the field. Which is of course fake
> > for a periodic boundary.
> >
> > If you're set on doing e.g. permeation studies that require applying a
> > particular voltage across the box, external fields aren't really the way
> to
> > go. Gromacs has a built-in computational electrophysiology (called
> CompEl,
> > I think) protocol as part of the package. I've never used it, and it
> works
> > by artificially maintaining an ionic concentration gradient, but it could
> > be useful. The issue with zero actual correspondence between external
> > fields and actual voltage drops isn't specific to Gromacs -- it's all
> part
> > of Ewald sum legacy with electrostatics. I am only aware of one software
> > suite that precisely solves Poisson on a real-space 3-D multigrid, but
> it's
> > neither free, nor available to the public in any way.
> >
> > Alex
> >
> >
> >
> > On 3/22/2018 4:59 AM, Shreyas Kaptan wrote:
> >
> >> Okay. But then how can one confirm that the correct potential is applied
> >> if
> >> not by looking at the charge distribution?
> >>
> >> Shreyas
> >>
> >> On Thu, Mar 22, 2018, 00:32 Alex <nedomacho at gmail.com> wrote:
> >>
> >> No, you are exactly right -- it does NOT include the external field
> >>> explicitly. The external field acts as a magical force here and gmx
> >>> potential would produce a potential distribution based on the resulting
> >>> charge distribution. The external field itself, once again, however,
> does
> >>> not exist in that picture. I mean, you could add it as a linear drop of
> >>> potential from one end to the other, but that is purely artificial. I
> >>> stay
> >>> away as much as possible from plotting charge distributions from
> >>> simulations steered by external fields.
> >>>
> >>> Alex
> >>>
> >>> On Wed, Mar 21, 2018 at 4:29 PM, Shreyas Kaptan <
> shreyaskaptan at gmail.com
> >>> >
> >>> wrote:
> >>>
> >>> I am confused about which potential it actually calculates. As I
> >>>> understand, the electric field (external) adds a force for each
> charged
> >>>> particle. This ought to change the ion distribution. If I read the gmx
> >>>> potential documentation right, it uses the distribution of the charges
> >>>> in
> >>>> the box to calculate the electrostatic potential in the box. Should
> that
> >>>> not include the external field-induced potential? I admit, that I
> >>>> assumed
> >>>> that this was the dominant part of the potential.
> >>>>
> >>>> Was I wrong?
> >>>>
> >>>> Shreyas
> >>>>
> >>>> On Wed, Mar 21, 2018 at 11:16 PM, Alex <nedomacho at gmail.com> wrote:
> >>>>
> >>>> It does exactly what it says it does. Which part is misunderstood?
> >>>>>
> >>>>> Alex
> >>>>>
> >>>>> On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan <
> >>>>>
> >>>> shreyaskaptan at gmail.com
> >>>
> >>>> wrote:
> >>>>>
> >>>>> Hi.
> >>>>>>
> >>>>>> Thanks for the reply! Maybe I misunderstood the tool documentation.
> >>>>>>
> >>>>> So
> >>>
> >>>> what
> >>>>>
> >>>>>> does it *really* do?
> >>>>>>
> >>>>>> On Wed, Mar 21, 2018 at 8:27 PM, Alex <nedomacho at gmail.com> wrote:
> >>>>>>
> >>>>>> Also, here is a message for the authors of the documentation:
> >>>>>>>
> >>>>>>> *-[no]spherical*(no)
> >>>>>>>
> >>>>>>>     Calculate spherical thingie
> >>>>>>>
> >>>>>>> Come on, guys. :)
> >>>>>>>
> >>>>>>> Alex
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On 3/21/2018 1:24 PM, Alex wrote:
> >>>>>>>
> >>>>>>> Two things:
> >>>>>>>>
> >>>>>>>> 1. We cannot see your attachment, upload to a file share.
> >>>>>>>>
> >>>>>>>> 2. gmx potential does not reveal the actual potential drop due to
> >>>>>>>> external electric field itself. What it does instead is described
> >>>>>>>>
> >>>>>>> in
> >>>
> >>>> the
> >>>>>
> >>>>>> utility documentation.
> >>>>>>>>
> >>>>>>>> Alex
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On 3/21/2018 12:42 PM, Shreyas Kaptan wrote:
> >>>>>>>>
> >>>>>>>> Dear GMX users,
> >>>>>>>>>
> >>>>>>>>> I am trying to use the gmx potential tool to calculate the
> >>>>>>>>>
> >>>>>>>> potential
> >>>>
> >>>>> created by applying a constant electric field in the Z-direction.
> >>>>>>>>>
> >>>>>>>>> I am using the 2018 gromacs version. The electric field was
> >>>>>>>>>
> >>>>>>>> applied
> >>>
> >>>> with:
> >>>>>>
> >>>>>>>
> >>>>>>>>> electric-field-z         = 0.00625 0 0 0; 0.1 V voltage for 160
> >>>>>>>>>
> >>>>>>>> angstrom
> >>>>>>
> >>>>>>> Z
> >>>>>>>>> len
> >>>>>>>>>
> >>>>>>>>> When I use the gmx potential (from 2016.1 version) on the result
> >>>>>>>>>
> >>>>>>>> of
> >>>
> >>>> the
> >>>>>
> >>>>>> simulation, I get the attached output.  I am not sure how to
> >>>>>>>>>
> >>>>>>>> interpret
> >>>>>
> >>>>>> the
> >>>>>>>>> result. I expected a 100 V potential drop across the box, but I
> >>>>>>>>>
> >>>>>>>> do
> >>>
> >>>> not
> >>>>>
> >>>>>> s
> >>>>>>
> >>>>>>> that. Is that an error on part of my interpretation or is there
> >>>>>>>>>
> >>>>>>>> something
> >>>>>>
> >>>>>>> wrong with my setup?
> >>>>>>>>>
> >>>>>>>>> Thanks in advance!
> >>>>>>>>>
> >>>>>>>>> Shreyas
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> --
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> >>>>>>>
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> >>>>
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> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Shreyas Sanjay Kaptan
> >>>>>> --
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> >>>>>>
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> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> Shreyas Sanjay Kaptan
> >>>> --
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>
>
> --
> Shreyas Sanjay Kaptan
> --
> Gromacs Users mailing list
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