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 - 07:35:41 CDT

There is large deviations of real temperations from target temperatures.
I used following options for REMD:
 &cntrl
    imin = 0, irest = 0, ntx = 1, nstlim = 250, dt = 0.001,
    ntt = 3, gamma_ln = 1.0, ig = -1,
    tempi = 0.0, temp0 = 261.6,
    ntc = 2, ntf = 2, tol = 0.00001, ntb = 0, ntr = 0,
    ntwx = 250, ntwe = 0, ntwr =250, ntpr = 250, nscm = 1000,
    igb=5, gbsa=1, cut = 999., rgbmax = 999.,
    numexchg=40000,
 /

Should I set gamma_ln to 4.0, so it is synchronous with nstlim=250 and dt=0.0001?

        
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 20:14:36 Carlos Simmerling wrote=======

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

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

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