AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 10 2008 - 07:00:58 CDT

as I've mentioned in a few recent amber mailing list replies,
tslop3.f was meant as an easy way to generate very quick
and approximate temperatures, assuming nothing complicated
and particularly no phase transitions. it certainly does not
make any effort to optimize the REMD efficiency as has been
described in several recent papers. it's just for basic testing
and simple systems, and users should expect to have to put
in more work on their own to optimize the T distribution.

2008/7/10 Ye Mei <ymei_at_itcc.nju.edu.cn>:
> The temperatures are generated using tslop3.f found in the amber tutorial. The energy distribution and the overlap seem OK to me, which can be seen in the attached file.
>
>
> 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
>
>
> ======= 2008-07-10 19:01:05 Carlos Simmerling wrote=======
>
>>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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>>
>>
>>
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