ions behavior in protein-water box:

From: Emanuelle Bachelet (emanuellebachelet_at_gmail.com)
Date: Wed Oct 29 2008 - 13:44:59 CDT

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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