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

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 10 Jul 2008 09:11:33 -0400

I don't see any obvious problems, though I would do
some things differently like explicitly setting ig.
this gamma should be fine. my guess is that
there are some low energy basins that increase
the energy gap from the average structures and cause
problems with exchange. however, that should be obvious in
the energies and doesn't appear so from your histograms.
if they are really from only the subset of time where you
have trouble with exchanges, then something else must be
wrong. if you plot all of the temperature histories of the
replicas and see partitioning of them, then you should
look more closely at the exchange success between the
temperature(s) where there are not many successful
temperature transitions and see what the energies are doing.
you may simply need to add additional temperatures in that
region. it also may be that the low energy structures will indeed
get sent to low T, and stay there until the higher temperature
runs locate even better structures. this can be a cause of slow
convergence.


2008/7/10 Ye Mei <ymei.itcc.nju.edu.cn>:
> 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.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.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.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 usersúČ
>>>>>>>
>>>>>>> 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
>>>>>>>
>>>>>>> -----------------------------------------------------------------------
>>>>>>> The AMBER Mail Reflector
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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
>>>>>>===================================================================
>>>>>>-----------------------------------------------------------------------
>>>>>>The AMBER Mail Reflector
>>>>>>To post, send mail to amber.scripps.edu
>>>>>>To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>>>>> to majordomo.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.gmail.com
>>>>Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>>>>===================================================================
>>>>-----------------------------------------------------------------------
>>>>The AMBER Mail Reflector
>>>>To post, send mail to amber.scripps.edu
>>>>To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>>> to majordomo.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.gmail.com
>>Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>>===================================================================
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>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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> The AMBER Mail Reflector
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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
===================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo.scripps.edu
Received on Sun Jul 13 2008 - 06:07:27 PDT
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