AMBER Archive (2008)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Thu Jul 10 2008 - 06:16:59 CDT

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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