[gmx-users] Ion in simulation

[Ran Friedman]

In addition to what Andreas wrote:
1. You need to have a neutral system when you work with PME.
2. Even if the system is neutral, you may want to add some excess ions in order to screen some of the interactions between charged side chains.

Ran.

Andreas Kukol 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
> Andreas
>
> >>> 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.
>
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--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
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