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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu