[gmx-users] Ion in simulation

Eric Jakobsson jake at ncsa.uiuc.edu
Sun Feb 8 22:48:00 CET 2004

A box the size of our simulation cells in electrolyte is not always 
instantaneously electroneutral, but it is electroneutral averaged over 
time; there is no systematic sustained net charge.  A good rule of thumb is 
that if the size of the simulation cell is greater than a Debye length, 
then you should be sure to have electroneutrality in the simulation.  For 
physiological ionic strengths, the Debye length is about 8 angstroms, which 
is quite a small simulation cell, so in general you should have 
electroneutrality in order to simulate reality well.


At 04:23 PM 2/3/2004 +0000, you wrote:
>Dear Itamar,
>Unfortunately the small box is not the real world, but we would like it to 
>be as real as possible. Therefore I think adding ions to neutralise the 
>system is important.
>Also think about periodic boundary conditions creating an infinitly large 
>system, which we would not expected to be charged.
>If you explicitly wan't to simulate a single molecule, e.g. ionic 
>complexes in the gas phase, single ion channel events or compare with 
>atomic force microscopy measurements charged systems might be useful 
>(although I am not sure).
>Best wishes
> >>> ikass at cc.huji.ac.il 03/02/2004 16:03:32 >>>
>    Hi all, in the system I have protein in membrane, DMPC and water, and
>the net charge is -2, were the simulation box is
>6.1082x6.1082x6.6675nm.  In the literature I see that people add ions
>in order to prevent net charge in the system (etc. Forrest et. al. 2000
>Biophys J. 78:55-69).
>    My question is does it important?  After all, in the real world such
>small box does not has net charge of zero 100% of the time.
>    thanks, Itamar.
>Computers are like airconditioners... They don't work well with Windows
>| 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:
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

(Currently on leave to NIH to serve as Director of Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medical Sciences and Chair of the NIH Biomedical Information 
Science and Technology Initiative Consortium.  Usual schedule is four days 
a week at NIH and three days a week at Illlinois.)

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