AMBER: Regarding counter ions

From: Rafi Ahmad <>
Date: Wed, 14 Mar 2007 21:00:59 +0100

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.
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Received on Sun Mar 18 2007 - 06:07:11 PDT
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