[gmx-users] gmx potential

[Shreyas Kaptan]

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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