Another question about MD simulation of a domain.

From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Tue Sep 27 2005 - 12:30:43 CDT

Hi all. Another question is, if I put a domain in a solvent box, with the solvent preequilibrated, and start the simulation, why is the energy suddenly extremely high? Shall I add ions of a buffer solution? I just don't know how to solve the charge problems, and how to start the simulation of a given protein structure.
 
Thanks.
Boyang.

                
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