AMBER Archive (2008)

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

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Thu Jul 10 2008 - 07:11:28 CDT


Yeah, I read that mail.
Thank you very much.

        
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 20:02:42 Carlos Simmerling wrote=======

>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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