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 - 06:23:39 CDT

are these histograms taken over the time period where exchanges
are not happening?

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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>>
>>
>>
>>--
>>===================================================================
>>Carlos L. Simmerling, Ph.D.
>>Associate Professor Phone: (631) 632-1336
>>Center for Structural Biology Fax: (631) 632-1555
>>CMM Bldg, Room G80
>>Stony Brook University E-mail: carlos.simmerling_at_gmail.com
>>Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>>===================================================================
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>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
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