[gmx-users] Ion in simulation

Andreas Kukol A.Kukol at warwick.ac.uk
Tue Feb 3 17:24:01 CET 2004

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 
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