AMBER Archive (2008)

Subject: Re: AMBER: analysis REMD

From: rebeca_at_mmb.pcb.ub.es
Date: Wed May 21 2008 - 12:03:59 CDT

No, I have taken this into account, so rotation and translation has been
removed, but thank you anyaway.
Rebeca.

Quoting Adrian Roitberg <roitberg_at_qtp.ufl.edu>:

> Rebeca,
> How are you doing the RMS calculation ?
>
> is it possible that you are computing the RMSD WITHOUT rotation and
> translation taken out ?
>
> What you are seeing might simply be an effect of that.
>
>
> a.
>
>
> 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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>>
>>
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
> ============================================================================
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