Re: ions behavior in protein-water box:

From: Emanuelle Bachelet (
Date: Wed Oct 29 2008 - 16:56:10 CDT

Hi Chris,

By closer I mean less than 5A, I haven't measured the exact distance because
it's fluctuating. But imo, less than 5A means ions are going to modify the
electrostatic interactions with/on the protein. Ions should be just to
neutralize the system not to interact with the protein.

I will also have a look at the reference you mention.


On Wed, Oct 29, 2008 at 4:05 PM, Christopher Gillespie <
> wrote:

> Ema,
> What exactly do you mean by "closer"? Ion association with protein
> surfaces is not necessarily an "incorrect" observation rather ions can
> interact with various parts routinely. Take a look at the work of Pavel
> Jungwirth on ion protein association.
> Best
> Chris
> On Oct 29, 2008, at 2:44 PM, Emanuelle Bachelet wrote:
> Hello,
>> I have a question regarding ions in a simulation.
>> I have a protein that has a net charge of -9 (it includes one of the
>> residues which is phosphorylated). I immersed this protein in water box it
>> and added 4 calcium ions and one sodium ion to neutralize the overall
>> charge.
>> But when my simulation system reaches .5ns of production dynamics (NVE),
>> some ions move closer to the protein. In my opinion, they should not come
>> too close to protein so as to modify the protein behavior. Does this mean
>> that I constrain the ions at a particular position?
>> thanks,
>> Ema.

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