[gmx-users] Counter ions problem

[Xavier Periole]

I don't think you want the counter ion interacting with the peptide.
Except if there is a specific binding site, of course. The counter ions 
are there to neutralize the system not to interact with the protein. 
In general you impose the counter ion to be a minimum distance
from the protein and you pray it not to mess up with your protein !!
It can result in big deformations of the protein !!

XAvier