A question about MD simulation of peptide.

From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Tue Sep 27 2005 - 12:24:59 CDT

Hi all. I just have a question about a basic concept of MD simulation of peptide.
     If all the side chains of a peptide are in their favorite charged state, a peptide might not be neutral. So if we simulate the folding process of this peptide in water solution, shall we just put this charged peptide in neutral water box, with periodic boundary condition, and nothing else, or
, shall we neutralize this peptide by adding counter ions with corresponding concentration in the solvent box?
     Thanks for your time!
Univ Illinois, Chicago.


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