Re: AMBER: simulated annealing

From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
Date: Wed, 28 Jul 2004 08:17:55 -0400

it looks like you didn't set nmropt=1 to read the weight changes.
it's always a very good idea to read the output file and make sure that
sander tells you that it will do what you wanted it to do. in this case,
did sander ever say it was going to change the temperature? the
output should have a section that describes all of the changes it thinks
you requested.

also check your group input- I don't think it is read either as I don't
see anything in the input that would need a group list. did you want
restraints, or what is that for?

===================================================================
Carlos L. Simmerling, Ph.D.
Assistant Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling.stonybrook.edu
===================================================================




Abd Ghani Bin Abd Aziz wrote:

> Dear amber,
> i've problem with my simulated annealing MD. i try to heat my
> structure up to 400K but the output file showed that the maximum
> temperature is 300K and the output file showed that the structure is
> not recool to 10K. at the end of the simulation, the temperature still
> maintain at 300K and it completed the timestep that i set (15ps). why
> the temperature is not achieve to 400K? and why it's not recool to 10K
> at the of simulation.
> Thank you
> cd /home/ghaneiee/1jkmsim
> cat << eof1 > simul_anneal.in
> # 15ps simulated protocol
> &cntrl
> nstlim=15000, ntt=1,
> scee=1.2, igb=0, ntb=2, ntp=1, ntc=2,
> ntpr=50, pencut=0.1,
> ipnlty=1, vlimit=40,
> &end
> #
> # Simple simulated annealing algorithm:
> #
> # from steps 0 to 1000: raise target temperature 10-400K
> # from steps 1000 to 3000: leave at 400K
> # from steps 3000 to 15000: re-cool to low temperature
> #
> &wt
> type='TEMP0', istep1=0, istep2=1000, value1=10.0, value2=400.0,
> &end
> &wt
> type='TEMP0', istep1=1001, istep2=3000, value1=400.0, value2=400.0,
> &end
> &wt
> type='TEMP0', istep1=3001, istep2=15000, value1=400.0, value2=10.0,
> &end
> #
> # Strength if temperature coupling:
> #
> # steps 0 to 3000: tight coupling for heating and equilibration
> # steps 3000 to 11000: slow cooling phase
> # steps 11000 to 13000: somewhat faster cooling
> # steps 13000 to 15000: fast cooling, like a minimization
> #
> &wt
> type='TAUTP', istep1=0,istep2=1000, value1=0.1,value2=0.1,
> &end
> &wt
> type='TAUTP', istep1=1001,istep2=2000,value1=0.1,value2=0.1,
> &end
> &wt
> type='TAUTP', istep1=2001,istep2=13000,value1=5.0,value2=5.0,
> &end
> &wt
> type='TAUTP', istep1=13001,istep2=14000,value1=4.0,value2=4.0,
> &end
> &wt
> type='TAUTP', istep=14001,istep2=15000,value1=3.0,value2=3.0,
> &end
> #
> # "Ramp up" the restraints over the first 3000 steps:
> #
> &wt
> type='REST', istep1=0,istep2=2000,value1=0.1,value2=1.0,
> &end
> &wt
> type='REST', istep1=2001,istep2=15000,value1=1.0,value2=1.0,
> &end
> &wt type='END'
> &end
> LISTOUT=POUT
> DISANG=RST.f
> # Group definition
> 20.0
> RES 101 270
> RES 291 365
> END
> END
> eof1
> /usr/local/amber6/exe/sander -O -i simul_anneal.in -o simul_anneal.out
> -p 1jkm.prm -c 1jkm_min5.xyz -ref 1jkm_min5.xyz -r simul_anneal.xyz -x
> simul_anneal.crd
> N01Eyh:)lzwfj)mz*inNrzǧv칻&jfޮ&j:+v⦛du==

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Received on Wed Jul 28 2004 - 13:53:01 PDT
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