AMBER Archive (2008)

Subject: Re: AMBER: replicas trapped in a few low temperatures

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 10 2008 - 05:59:03 CDT

have you compared the overlap of potential energy distributions for
the temperatures? perhaps your spacing is not correct and the energy gap
is too large for successful exchange.

2008/7/10 Ye Mei <ymei_at_itcc.nju.edu.cn>:
> 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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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
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