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 - 06:07:44 PDT
