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 <nedoma...@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 <shreyaskap...@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 <nedoma...@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 <
shreyaskap...@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 <nedoma...@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
--
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.
--
Shreyas Sanjay Kaptan
--
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
* 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.
--
Shreyas Sanjay Kaptan
--
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
* 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
* 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.
