AMBER Archive (2008)

Subject: Re: AMBER: analysis REMD

From: rebeca_at_mmb.pcb.ub.es
Date: Tue May 20 2008 - 13:31:30 CDT

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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