AMBER Archive (2008)

Subject: Re: AMBER: analysis REMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed May 21 2008 - 12:18:06 CDT

I think >2500 atoms with REMD has not been well established
as far as convergence properties, so you will need to proceed very
carefully. I would suggest working on a smaller system until
you are really comfortable with REMD, and then move to a
system that would probably be as large as anything other
REMD application reported so far. The main question is whether
reversible unfolding of your protein can be observed during the
MD runs, even at higher temperatures. I think it will be
very interesting but is certainly a research challenge from the
method point of view. Except to have to do very long runs and lots
of convergence analysis.

On Tue, May 20, 2008 at 2:31 PM, <rebeca_at_mmb.pcb.ub.es> wrote:
> Thanks a lot for the information.
> I get the temperatures from the "Temperature generator for REMD-simulations"
> (Alexandra Patriksson and David van der Spoel, A temperature predictor for
> parallel tempering simulations Phys. Chem. Chem. Phys., 10 pp. 2073-2077
> (2008)). It gives a supposed range of temperatures in base of the size of
> the
> simulated system (my protein has about 2573 atoms).
> You mention I should create a graphic of energy versus temperature. What
> temperature should I consider, those one that appear in the "info" file, do
> I?
> In the attached file, you can see this representation for the case of the
> first
> temperature for the case I put in the forum, implicit solvent. What should I
> conclude from this graphic? The variation of temperature is quite high, is
> it
> normal?
> Anyway, I have also tried REMD of the same protein but solvated (using
> explicit
> solvent) I do not see any of these stange jumps. The rmsd for the
> trayectories
> in this case are not higher than 3 A. Do you think the jumps mention could
> be a
> effect of not-solvation?
>
> Thank you very much for your help. It is very helpful due to the small
> amount of
> tutorial documentation about REMD existent for inexpert users.
>
> Rebeca García Fandiño
> rebeca_at_mmb.pcb.ub.es
>
>
> Quoting Carlos Simmerling <carlos.simmerling_at_gmail.com>:
>
>> those changes are probably from the exchanges, you can compare the jump
>> times
>> with the exchange if you want to make sure.
>> as far as whether the protein should unfold, the populations are only
>> "correct"
>> after convergence. they may be completely wrong near the start.
>> the RMSD is very large- is this a large protein? have you seen any reports
>> in the literature of REMD for such a large system? if not, then you should
>> learn REMD well on a small peptide first before trying something that
>> is at the limit or beyond what is possible.
>> also, how did you choose your temperatures? did you create energy vs
>> temperature plots? spacing depends strongly on system size, so be
>> careful how you select them.
>>
>> good luck!
>>
>> On Mon, May 19, 2008 at 2:41 PM, rebeca <rebeca_at_mmb.pcb.ub.es> wrote:
>>>
>>> Hello,
>>> I am new in Replica Exchange simulations. I am trying to simulate the
>>> unfolding of a protein, using REMD and implicit solvent.
>>> I chose 10 different temperatures, and this inputs file such as this (The
>>> difference between them is only temp0, which goes from 300K to 417K):
>>>
>>> Title Line
>>> &cntrl
>>> imin = 0, nstlim = 100000, dt = 0.002,
>>> ntx = 5, tempi = 0.0, temp0 = 300.00,
>>> ntt = 3, tol = 0.000001, gamma_ln = 1.0,
>>> ntc = 2, ntf = 1, ntb = 0,
>>> ntwx = 500, ntwe = 0, ntwr =500, ntpr = 100,
>>> scee = 1.2, cut = 99.0,
>>> ntr = 0, tautp = 0.1, offset = 0.09,
>>> nscm = 500, igb = 5, irest=1,
>>> ntave = 0, numexchg=5,
>>> &end
>>>
>>> After the calculation the rem.log file is this one:
>>>
>>> rem.log:
>>>
>>
>>> # replica exchange log file
>>> # numexchg is 5
>>> # Replica #, Velocity Scaling, T, Eptot, Temp0, NewTemp0, Success rate
>>> (i,i+1)
>>> # exchange 1
>>> 1 1.18 0.00 -5916.54 300.00 417.26 0.00
>>> 2 1.02 0.00 -5916.54 311.77 323.86 2.00
>>> 3 0.98 0.00 -5916.54 323.86 311.77 0.00
>>> 4 1.02 0.00 -5916.54 336.23 348.91 2.00
>>> 5 0.98 0.00 -5916.54 348.91 336.23 0.00
>>> 6 1.02 0.00 -5916.54 361.90 375.23 2.00
>>> 7 0.98 0.00 -5916.54 375.23 361.90 0.00
>>> 8 1.02 0.00 -5916.54 388.89 402.90 2.00
>>> 9 0.98 0.00 -5916.54 402.90 388.89 0.00
>>> 10 0.85 0.00 -5916.54 417.26 300.00 2.00
>>> # exchange 2
>>> 1 -1.00 422.71 -3536.10 417.26 417.26 1.00
>>> 2 -1.00 329.49 -4430.31 323.86 323.86 0.00
>>> 3 -1.00 303.86 -4488.56 311.77 311.77 1.00
>>> 4 1.02 353.18 -4141.47 348.91 361.90 1.00
>>> 5 -1.00 339.42 -4319.97 336.23 336.23 1.00
>>> 6 -1.00 369.33 -3999.84 375.23 375.23 0.00
>>> 7 0.98 366.69 -4180.50 361.90 348.91 1.00
>>> 8 -1.00 405.83 -3678.84 402.90 402.90 0.00
>>> 9 -1.00 396.82 -3762.25 388.89 388.89 1.00
>>> 10 -1.00 299.20 -4597.24 300.00 300.00 0.00
>>> # exchange 3
>>> 1 -1.00 411.00 -3383.81 417.26 417.26 0.67
>>> 2 -1.00 323.04 -4404.75 323.86 323.86 0.00
>>> 3 -1.00 314.74 -4497.58 311.77 311.77 0.67
>>> 4 -1.00 368.70 -4051.83 361.90 361.90 0.67
>>> 5 -1.00 341.82 -4302.80 336.23 336.23 0.67
>>> 6 -1.00 380.67 -3803.52 375.23 375.23 0.00
>>> 7 -1.00 347.26 -4174.54 348.91 348.91 0.67
>>> 8 -1.00 394.91 -3642.40 402.90 402.90 0.00
>>> 9 -1.00 392.82 -3745.85 388.89 388.89 0.67
>>> 10 -1.00 307.94 -4588.30 300.00 300.00 0.00
>>> # exchange 4
>>> 1 -1.00 416.80 -3485.65 417.26 417.26 0.50
>>> 2 -1.00 322.18 -4457.13 323.86 323.86 0.00
>>> 3 -1.00 309.32 -4511.51 311.77 311.77 0.50
>>> 4 -1.00 358.27 -3924.67 361.90 361.90 0.50
>>> 5 -1.00 332.14 -4260.49 336.23 336.23 0.50
>>> 6 -1.00 370.26 -3840.88 375.23 375.23 0.00
>>> 7 -1.00 349.41 -4135.59 348.91 348.91 0.50
>>> 8 -1.00 407.47 -3554.56 402.90 402.90 0.00
>>> 9 -1.00 387.76 -3712.64 388.89 388.89 0.50
>>> 10 -1.00 311.37 -4549.89 300.00 300.00 0.00
>>> # exchange 5
>>> 1 -1.00 417.87 -3565.83 417.26 417.26 0.40
>>> 2 -1.00 331.00 -4332.42 323.86 323.86 0.00
>>> 3 -1.00 314.23 -4455.65 311.77 311.77 0.40
>>> 4 -1.00 361.23 -3900.19 361.90 361.90 0.40
>>> 5 1.02 331.34 -4280.28 336.23 348.91 0.80
>>> 6 -1.00 378.91 -3800.95 375.23 375.23 0.00
>>> 7 0.98 358.27 -4240.73 348.91 336.23 0.40
>>> 8 0.98 398.57 -3712.53 402.90 388.89 0.00
>>> 9 1.02 396.72 -3736.43 388.89 402.90 0.80
>>> 10 -1.00 303.86 -4591.79 300.00 300.00 0.00
>>>
>>> When I look at the trayectory, the result is very strange (you can see
>>> the
>>> rms of replica 1 in the attached file). There are very strange jumps in
>>> the
>>> RMS, more than 30 A. When I visualize the trayectory in VMD I can see
>>> that
>>> these jumps correspond to the unfolded structure, but when the jumps
>>> finish, the folded structure appears again. I am usin repcrd = 0, as you
>>> can see, so I obtain the history of a temperature. At a same temperature,
>>> should it exist these types of changes?
>>>
>>> Please, could anyone help me with these simulations? Is this normal?
>>> Perhaps is it a problem of the selection of temperatures?
>>>
>>> Thank you very much in advance,
>>>
>>> Rebeca García Fandiño
>>> Parc Cientific de Barcelona
>>> rebeca_at_mmb.pcb.ub.es
>>>
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>
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
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