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.