AMBER Archive (2009)

Subject: Re: [AMBER] Simulated annealing

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 25 2009 - 19:31:30 CST

check tempi- unless it is greater then 0 ig won't set velocities. also
you might want ntt equal 3 using langevin dynamics, then ig will
change the thermostat.

On 2/25/09, Ibrahim Moustafa <I.moustafa_at_psu.edu> wrote:
> Dear all,
>
> Iım trying to run a Simulated Annealing for a protein in which two loops
> missing from the crystal structure are modeled.
> Those regions from the structure are restrained. I use the GB model for the
> simulation using the input file given below.
> The plan was to apply the SA for 10 cycles, each starting with a new set of
> velocities by changing ³ig values² every time randomly. The simulation runs
> fine; BUT the output is exactly the same for all simulations. I expected to
> see different trajectories in the different simulations. This repetitive
> behavior
> is odd suggesting that something is not right going on. Two examples for
> the output from two runs are shown below.
> Iıd appreciate if someone can point me to why I see this behavior during SA?
> And what is faulty in the protocol used?
> This simulation starts using a restart file from 50 ps MD to bring the
> system from 0-300 K. Originally, I used ³irest=1² as in the tutorial of Dr.
> Ross
> and saw the same behavior. Then, I tried ³irest=0² but it did not solve the
> problem.
>
>
> > INPUT FILE
>
> &cntrl
> imin=0, irest=0, ntx=5,
> nstlim=200000, dt=0.0005,
> ntpr=500, ntwx=10000, ntwr=1000,
> ntt=1,
> ntc=2, ntf=2,
> ntb=0, nsnb=10, scee=1.2,
> ntr=1, restraint_wt=10, restraintmask=':1-134 | :145-183 | :200-628',
> cut=25, rgbmax=25, ntb=0, igb=5, vlimit=10, ig=600129,
> nmropt=1,
> &end
> &ewald
> eedmeth=5,
> &end
> &wt
> type='TEMP0', istep1=0, istep2=20000,
> value1=300, value2=800,
> &end
> &wt
> type='TEMP0', istep1=20001, istep2=60000,
> value1=800, value2=800,
> &end
> &wt
> type='TEMP0', istep1=60001, istep2=200000,
> value1=800, value2=300,
> &end
> # Strength of Temp coupling
> # Step 0 to 6000: very fast heating
> # Step 60001 to 160000: slow cooling
> # Step 160001 to 180000: faster cooling
> # Step 180000 to 200000: very fast cooling
> &wt
> type='TAUTP', istep1=0, istep2=60000,
> value1=0.05, value2=0.05,
> &end
> &wt
> type='TAUTP', istep1=60001, istep2=160000,
> value1=1.0, value2=1.0,
> &end
> &wt
> type='TAUTP', istep1=160001, istep2=180000,
> value1=0.5, value2=0.5,
> $end
> &wt
> type='TAUTP', istep1=180001, istep2=200000,
> value1=0.05, value2=0.05,
> &end
> &wt
> type='END',
> &END
> /
>
> _____________________________________________________
>
>
> OUTPUT RUN-1
>
> NSTEP = 500 TIME(PS) = 50.250 TEMP(K) = 310.73 PRESS =
> 0.0
> Etot = -10363.4854 EKtot = 7777.7343 EPtot =
> -18141.2197
> BOND = 1916.0569 ANGLE = 4459.8222 DIHED =
> 6585.8885
> 1-4 NB = 2179.8858 1-4 EEL = 20755.1795 VDWAALS =
> -5485.6124
> EELEC = -42119.8223 EGB = -8122.6770 RESTRAINT =
> 1690.0591
> EAMBER (non-restraint) = -19831.2788
> ---------------------------------------------------------------------------
> ---
>
> OUTPUT RUN-2
>
> NSTEP = 500 TIME(PS) = 50.250 TEMP(K) = 310.73 PRESS =
> 0.0
> Etot = -10363.4854 EKtot = 7777.7343 EPtot =
> -18141.2197
> BOND = 1916.0569 ANGLE = 4459.8222 DIHED =
> 6585.8885
> 1-4 NB = 2179.8858 1-4 EEL = 20755.1795 VDWAALS =
> -5485.6124
> EELEC = -42119.8223 EGB = -8122.6770 RESTRAINT =
> 1690.0591
> EAMBER (non-restraint) = -19831.2788
> ---------------------------------------------------------------------------
> ---
>
>
>
> Many thanks in advance for your useful comments and help.
>
> thanks,
> Ibrahim
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80           Phone: (631) 632-1336   Fax: 632-1555
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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