AMBER Archive (2005)

Subject: AMBER: keeping two domains closed together during a simulation

From: Sergio E. Wong (swon9_at_itsa.ucsf.edu)
Date: Thu May 05 2005 - 19:44:45 CDT

Dear amber users;

   I'm simulating a protein (antibody) that has two domains. I'm
concerned about the two domains drifting away during the simulation and so
I want to impose some sort of potential to keep them close to each other.
Is there a way to restrain the center of mass rather than specific atoms??

Thanks

-Sergio

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