AMBER Archive (2008)

Subject: Re: AMBER: analysis REMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 20 2008 - 01:51:22 CDT

which amber version? REMD has changed with versions so
we need that info.
thanks

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
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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