AMBER Archive (2007)Subject: AMBER: Regarding counter ions
From: Rafi Ahmad (Rafi.Ahmad_at_fagmed.uit.no)
Date: Wed Mar 14 2007 - 14:00:59 CST
Dear Amber users,
I am doing a simulation for a protein-DNA interaction. To neutralise the complex I need to add 36 Na+ ions.
I was thinking that whether these ions affect the simulation results as there are soo many of them. As some of the simulation results that I see may be also attributed to Na+ ions.
Is is ok if I run the MD without counter ions?
Thanks in advance for your reply.
Regards
Rafi
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