[gmx-users] Electric potential over the membrane

[Itamar Kass]

    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).
                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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| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
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