AMBER Archive (2009)

Subject: Re: [AMBER] Simulated annealing

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 15 2009 - 06:43:56 CDT

What does the sander output say when it reads your input? Does it give
info saying it will change the thermostat?

I don't think you can combine igb=1 with eedmeth commands- check to
see if sander actually states it is doing this.

On Oct 15, 2009, at 6:59 AM, waleed zalloum <waleed_zalloum_at_yahoo.com>
wrote:

> Dear Amber users,
>
> I am calculating a 3D structure of a oligopeptide conjugated to
> single stranded DNA. I run NMR restrained simulated annealing. I
> specified certain heat range for certain number of steps ( as in the
> input file bellow). Upon running, the heat does not stick to the
> specified number of steps and there is a huge fluctuation in the
> temperature (eg. from 600 going to 800 and then go back to 650).
> What is the problem? is there any problem in the input file?
>
> I specified the LISTOUT option, but I don't get any output list
> coming after the end of simulation? what is the problem in that?
>
> ps. Bellow is the annealing input file.
>
> Thank you
>
>
>
> Waleed
>
> &cntrl
> nstlim=190000, pencut=-0.001, nmropt=1,ipnlty=1,scee=1.2,
> ntpr=200, ntt=3, ntwx=200,imin=0,gamma_ln=1.0,irest=0,ntx=1,
> cut=9.0, ntb=0, vlimit=10, dt=0.001, igb=1, ntc=2, ntf=2,temp0=500
> /
> &ewald
> eedmeth=5,
> /
> #
>
> &wt type='TEMP0', istep1=0,istep2=2000,value1=500.0,
> value2=500.0, /
> &wt type='TEMP0', istep1=2001, istep2=5000, value1=500.0,
> value2=1000.0, /
> &wt type='TEMP0', istep1=5001, istep2=10000, value1=1000.0,
> value2=1000.0, /
> &wt type='TEMP0', istep1=10001, istep2=20000.0, value1=1000.0,
> value2=950.0, /
> &wt type='TEMP0', istep1=20001, istep2=30000.0, value1=950.0,
> value2=900.0, /
> &wt type='TEMP0', istep1=30001, istep2=40000.0, value1=900.0,
> value2=850.0, /
> &wt type='TEMP0', istep1=40001, istep2=50000, value1=850.0,
> value2=800.0, /
> &wt type='TEMP0', istep1=50001, istep2=60000, value1=800.0,
> value2=750.0, /
> &wt type='TEMP0', istep1=60001, istep2=70000, value1=750.0,
> value2=700.0, /
> &wt type='TEMP0', istep1=70001, istep2=80000, value1=700.0,
> value2=650.0, /
> &wt type='TEMP0', istep1=80001, istep2=90000, value1=650.0,
> value2=600.0, /
> &wt type='TEMP0', istep1=90001, istep2=100000, value1=600.0,
> value2=550.0, /
> &wt type='TEMP0', istep1=100001, istep2=110000, value1=550.0,
> value2=500.0, /
> &wt type='TEMP0', istep1=110001, istep2=120000, value1=500.0,
> value2=450.0, /
> &wt type='TEMP0', istep1=120001, istep2=130000, value1=450.0,
> value2=400.0, /
> &wt type='TEMP0', istep1=130001, istep2=140000, value1=400.0,
> value2=350.0, /
> &wt type='TEMP0', istep1=140001, istep2=150000, value1=350.0,
> value2=300.0, /
> &wt type='TEMP0', istep1=150001, istep2=160000, value1=300.0,
> value2=250.0, /
> &wt type='TEMP0', istep1=160001, istep2=170000, value1=250.0,
> value2=200.0, /
> &wt type='TEMP0', istep1=170001, istep2=180000, value1=200.0,
> value2=150.0, /
> &wt type='TEMP0', istep1=180001, istep2=190000, value1=150.0,
> value2=100.0, /
>
>
> &wt type='TAUTP', istep1=0,istep2=10000,value1=0.4,
> value2=0.4, /
> &wt type='TAUTP', istep1=10001,istep2=170000,value1=4.0,
> value2=4.0, /
> &wt type='TAUTP', istep1=170001,istep2=180000,value1=1.0,
> value2=1.0, /
> &wt type='TAUTP', istep1=180001,istep2=190000,value1=0.1,
> value2=0.1, /
>
> &wt type='REST', istep1=0,istep2=5000,value1=0.0,
> value2=0.0, /
> &wt type='REST', istep1=5001,istep2=10000,value1=0.0,
> value2=0.01, /
> &wt type='REST', istep1=10001,istep2=20000,value1=0.01,
> value2=0.1, /
> &wt type='REST', istep1=20001,istep2=30001,value1=0.1,
> value2=0.15, /
> &wt type='REST', istep1=30001,istep2=40000,value1=0.15,
> value2=0.2, /
> &wt type='REST', istep1=40001,istep2=50000,value1=0.2,
> value2=0.25, /
> &wt type='REST', istep1=50001,istep2=60000,value1=0.25,
> value2=0.3, /
> &wt type='REST', istep1=60001,istep2=100000,value1=0.3,
> value2=0.6, /
> &wt type='REST', istep1=100001,istep2=150000,value1=0.6,
> value2=0.9, /
> &wt type='REST', istep1=150001,istep2=190000,value1=0.9,
> value2=1.0, /
>
> &wt type='END' /
> LISTOUT=POUT
> DISANG=RST
>
>
>
>
>
>
>
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