[gmx-users] Electric potential over the membrane

[David]

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 fields ad
> > > > > described in by Robertson & Tieleman at "The molecular basis of voltage
> > > > > gating of OmpF porin" (Biochem Cell Biol. 2002;80(5):517-23. ) of 
> > about
> > > > 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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> > > > > >--
> > > > > >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
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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
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++