[gmx-users] Electric potential over the membrane
Itamar Kass
ikass at cc.huji.ac.il
Sat Nov 22 11:02:01 CET 2003
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 ?
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
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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
> > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
> > >_______________________________________________
> > >gmx-users mailing list
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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
>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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