# [gmx-users] Electric potential over the membrane

David spoel at xray.bmc.uu.se
Sat Nov 22 12:04:01 CET 2003

```On Sat, 2003-11-22 at 11:45, Itamar Kass wrote:
>     Why the calculation is done over the membrane alone?  As I understand
> it, there is no start point to the electric fields, hence the and it spread
> all over the box, hence the calculation should inclose all the box (I have
> bilayers of DMPC between two water layers).

it *is* done over the whole box. You have a field E and each particle
with a charge q feels a force F = q E (F and E are vectors of course).
However, I just assumed you are interested in a potential over the
membrane, rather than the potential over the whole box.

>                 Kass.
>
>
> At 11:35 AM 11/22/2003, you wrote:
> >On Sat, 2003-11-22 at 11:23, Itamar Kass wrote:
> > >     I have periodic boundary, and the size of the box is
> > > ~6.2*6.2*6.7.  Follow from your explain I understand I have to write E_z =
> > > 1  15  0.0 the results potential will be 15mV/nm*6.7nm=~100mV?
> >except for a factor 1000, the unit is V/nm, so it should be 0.015
> >
> >Take care however that you should calculate the potential over your
> >membrane, not the box, so again for a 3 nm membrane with 100 mV you'd
> >want to use
> >
> >1 0.033 0.0
> >
> >
> >--
> >David.
> >________________________________________________________________________
> >David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> >Dept. of Cell and Molecular Biology, Uppsala University.
> >Husargatan 3, Box 596,          75124 Uppsala, Sweden
> >phone:  46 18 471 4205          fax: 46 18 511 755
> >spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
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>
>
> ********************************************
> Computers are like airconditioners... They don't work well with Windows
> open.
> ********************************************
>
> ===========================================
> | Itamar Kass
> | The Alexander Silberman
> | Institute of Life Sciences
> | Department of Biological Chemistry
> | The Hebrew University, Givat-Ram
> | Jerusalem, 91904, Israel
> | Tel: +972-(0)2-6585146
> | Fax: +972-(0)2-6584329
> | Email: ikass at cc.huji.ac.il
> | Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
> ============================================
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

```