AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 10 2008 - 07:12:51 CDT

this temperature distribution looks very unusual not not very
uniform. have you looked closely at them?
for example, starting at the lowest, there is a gap
of 9 degrees, then 40, then 15, then 30.

try restarting from the current set of restarts and run
a while longer to collect new exchange statistics and
energy profiles.

2008/7/10 Ye Mei <ymei_at_itcc.nju.edu.cn>:
> 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_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 19:26:44 Carlos Simmerling wrote=======
>
>>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
>>>>>
>>>>> -----------------------------------------------------------------------
>>>>> The AMBER Mail Reflector
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>>>>> to majordomo_at_scripps.edu
>>>>>
>>>>
>>>>
>>>>
>>>>--
>>>>===================================================================
>>>>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)
>>>> to majordomo_at_scripps.edu
>>>>
>>>
>>> = = = = = = = = = = = = = = = = = = = =
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>--
>>===================================================================
>>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)
>> to majordomo_at_scripps.edu
>>
>
> = = = = = = = = = = = = = = = = = = = =
>
>
>
>
>
>
> 

-- 
===================================================================
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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To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
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