AMBER Archive (2008)

Subject: AMBER: replicas trapped in a few low temperatures

From: Ye Mei (
Date: Thu Jul 10 2008 - 04:13:25 CDT

Dear Amber usersúČ

I am working on the folding of a small peptide using REMD in Amber 10. Sometimes, a replica finds a low energy conformation, then it is annealed to the lowest temperature. After that, this replica seems to be trapped in a few, maybe two or three, low temperatures, with a high "back exchange" frequency.
It there any suggestions that can make this replica sample more wide temperature space?

Best regards,

Ye Mei
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry of MOE
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093

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