Re: ion concentration in residue-based coarse-grained model

From: Francesco Oteri (
Date: Wed Sep 22 2010 - 03:50:41 CDT

If oyu don't specify anything,
autoionize add the required ions to neutralize your system.
If you would specify a concentration, in my opinion t is better to use
0.15M that is the phisiological ion concentration.
In this case autoionize will add an amount of atoms such to neutrilize
the system and to reache the desired concentration,

On 22/09/2010 09:49, Demet Akten wrote:
> Dear All,
> I have a system of membrane protein which is embedded in a POPC
> bilayer and solvated. I would like to ionize it, however, I am not
> sure what the value of the "ionic concentration" should be ? (0.01 for
> atomistic did not work, then I tried 0.1, and it neutralized the
> system, however I am not sure baout this value)
> Does anyone have any suggestions on that?
> Thanks you,
> Demet

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