AMBER Archive (2009)

Subject: [AMBER] Counter-ions

From: waleed zalloum (
Date: Thu Apr 02 2009 - 05:15:12 CDT

Dear Amber users,
I am running NMR restrained simulated annealing for a DNA/Protein conjugate. The system contains Li+ and perclorate as counter-ions. Upon exploring the .traj file, these counter-ions get far away from my system. How could I manage to keep them in the system.
Thank you,

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