[gmx-users] gmx potential

Shreyas Kaptan shreyaskaptan at gmail.com
Mon Apr 2 18:23:59 CEST 2018 

Hi.

Interestingly, I did exactly that compared it with the simulation without
an applied field and gmx potential does not seem to be consistent at
different times even after a 50ns early "equilibration".  I am not at work
today, but I will make the output available tomorrow.

On Mon, Apr 2, 2018 at 5:40 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>> Shreyas Sanjay Kaptan
> > >>>>>> --
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> > Shreyas Sanjay Kaptan
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-- 
Shreyas Sanjay Kaptan

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