AMBER Archive (2008)

Subject: AMBER: replicas trapped in a few low temperatures

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Thu Jul 10 2008 - 04:13:25 CDT

Dear Amber users£¬

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
ymei_at_itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry of MOE
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2008-07-10

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