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.mmb.pcb.ub.es
Quoting Carlos Simmerling <carlos.simmerling.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.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.mmb.pcb.ub.es
>>
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Received on Wed May 21 2008 - 06:07:50 PDT
