# [gmx-users] Electric potential over the membrane

Itamar Kass ikass at cc.huji.ac.il
Sat Nov 22 11:25:01 CET 2003

```    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?

At 11:15 AM 11/22/2003, you wrote:
>On Sat, 2003-11-22 at 11:00, Itamar Kass wrote:
> >     Hance, if the size of my system is about 6.7nm and I want a poteintial
> > of 100mv, the line will be E_z = 1  0.67  0.0 ?
>This line means 0.67 V/nm, so your potential over the whole box would be
>0.67*6.7 *if* it weren't for periodic boundary conditions. If you had
>6.7 nm and then a vacuum (i.e. an insulator) then you would have this
>potential.
>
> >
> >
> > At 10:57 AM 11/22/2003, you wrote:
> > >On Sat, 2003-11-22 at 10:46, Itamar Kass wrote:
> > > >     I guess I do not understand a basic issue here, why use mV/nm?
> > >
> > >because we can only apply an electric field, not a potential. Having a
> > >potential would imply having two electrodes or something like that.
> > >
> > > >
> > > > At 10:38 AM 11/22/2003, you wrote:
> > > > >On Sat, 2003-11-22 at 10:22, Itamar Kass wrote:
> > > > > >     O.K. David, no petty, what should I do to get an electric
> > > > > > described in by Robertson & Tieleman at "The molecular basis of
> voltage
> > > > > > gating of OmpF porin" (Biochem Cell Biol. 2002;80(5):517-23. ) of
> > > > > 300mV?
> > > > > >           thanks, Itamar.
> > > > >
> > > > >haven't read that, but if your membrane is, say, 3 nm wide, and
> you want
> > > > >a potential of 300mV, then 3 nm times 100 mV/nm would give you that,
> > > > >wouldn't it?
> > > > >
> > > > > >
> > > > > > >On Sat, 2003-11-22 at 09:01, Itamar Kass wrote:
> > > > > > > > Hi all,
> > > > > > > > It's a shame to me, but although I looked at the manual few
> > > times, I
> > > > > > > did not
> > > > > > > > understand how to used an electric potential.  I want to enter
> > > to my
> > > > > > > simulation
> > > > > > > > of peptide in a membrane an electric potential of ~100mV in
> the z
> > > > > > > direction (the
> > > > > > > > membrane normal).  My question is about the units, when I put
> > > > > > > > ;Electric field
> > > > > > > > E_z = 1  0.1  0.0
> > > > > > > > in my mdp file, does I get 100mV potential in my simulation?
> > > > > > >no, you get 100 mV/nm electric field.
> > > > > > >
> > > > > > > >    Thanks, Itamar.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > ********************************************
> > > > > > > > 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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> > > > > > > > _______________________________________________
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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
> > > > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++
> > > +++++
> > > > > > >
> > > > > > >_______________________________________________
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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
> > > > > > ============================================
> > > > > >
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list
> > > > > > gmx-users at gromacs.org
> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > >--
> > > > >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
> > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> +++++
> > > > >
> > > > >_______________________________________________
> > > > >gmx-users mailing list
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> > > > >Please don't post (un)subscribe requests to the list. Use the
> > > > >www interface or send it to gmx-users-request at gromacs.org.
> > > >
> > > >
> > > >
> > > > ********************************************
> > > > 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
> > > > ============================================
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
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> > > > www interface or send it to gmx-users-request at gromacs.org.
> > >--
> > >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
> > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
> > >_______________________________________________
> > >gmx-users mailing list
> > >gmx-users at gromacs.org
> > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > >Please don't post (un)subscribe requests to the list. Use the
> > >www interface or send it to gmx-users-request at gromacs.org.
> >
> >
> >
> > ********************************************
> > 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
> > ============================================
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
>--
>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
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.

********************************************
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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