[gmx-users] Counter ions problem

Xavier Periole periole at inka.mssm.edu
Tue Aug 19 18:43:01 CEST 2003

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 !!


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