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 - 06:49:08 CDT


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
>>>> 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
>===================================================================
>-----------------------------------------------------------------------
>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
>

= = = = = = = = = = = = = = = = = = = =
                        

       
 






-----------------------------------------------------------------------
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