AMBER Archive (2004)

Subject: AMBER: about amber8, replica exchange

From: J. Zhang, Dr (
Date: Fri May 28 2004 - 22:45:49 CDT

Dear Amber users,

I am very interested in the replica exchange MD in amber 8
However, after reading the user guide, I can not find
where I can change the exchange frequency between replicas,
I mean after how many MD steps amber will exchange replicas.

And another question:
When determining whether the exchange occurs, the potential
energy (E) of each replica must be known. Does amber use
the AVERAGE energy during the short running or the energy
of the last second? why?

Thank you very much.

Best Regards,

J. Zhang, Dr
Institute of Biophysics
Nanjing University

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