[gmx-users] gmx potential

[Shreyas Kaptan]

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
> > --
> > Gromacs Users mailing list
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-- 
Shreyas Sanjay Kaptan