Yes.
Two temperature-traveling figures are attached. The 10th replica seems OK, but the 14th has very limited traveling in temperature space.
And the last record in rem.log is as following:
# exchange 40000
1 -1.00 512.67 -305.27 519.20 519.20 0.36 -1
2 -1.00 350.22 -416.01 368.50 368.50 0.28 -1
3 -1.00 483.54 -364.33 452.70 452.70 0.36 -1
4 0.97 649.11 -237.76 637.70 595.50 0.00 -1
5 0.97 319.33 -490.05 321.30 300.00 0.27 -1
6 -1.00 380.46 -381.82 394.70 394.70 0.32 -1
7 0.97 255.57 -507.90 280.10 261.60 0.33 -1
8 -1.00 424.32 -354.12 422.70 422.70 0.35 -1
9 1.03 303.23 -491.52 300.00 321.30 0.31 -1
10 1.03 600.20 -217.64 595.50 637.70 0.37 -1
11 -1.00 555.93 -344.37 484.80 484.80 0.37 -1
12 -1.00 528.34 -289.41 556.00 556.00 0.37 -1
13 -1.00 363.72 -443.83 344.10 344.10 0.24 -1
14 1.03 264.68 -517.03 261.60 280.10 0.34 -1
the energy in the 14th replica is the lowest, and it is much higher in the 10th replica.
Best regards,
Ye Mei
ymei.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 19:26:44 Carlos Simmerling wrote=======
>are these histograms taken over the time period where exchanges
>are not happening?
>
>2008/7/10 Ye Mei <ymei.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.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.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.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.gmail.com
>>>Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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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.gmail.com
>Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>===================================================================
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>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo.scripps.edu
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Received on Sun Jul 13 2008 - 06:07:26 PDT
