AMBER Archive (2004)

Subject: AMBER: question on simulated annealing

From: Venkata S Koppuravuri (kvsuneel_at_linus.bmb.wright.edu)
Date: Tue Jul 27 2004 - 13:21:52 CDT

Hi All,

    I have a question regarding simulated annealing.
    Starting with a PDB file I have protonated and minimized my protein.
Following the example in the manual I have heated and cooled the protein
multiple times starting with the minimized protein (replicates ..... not
sequentially) using the minimized protein restart file. To my surprise
the structures in each replicate are identical. Since I wondered if
randomization of momentum occurred prior to annealing, I retried the
process doing replicate minimizations but got the same structures again. I
tried using the IG flag to change the random number seed between
annealing, but still go the same structure on all annealing runs.

    I was expecting that there would be some variation in the detailed
structure, corresponding to the structure finding alternative.... not
necessarily global .... minima. Is this not so? Or what am I missing in
doing my annealing?

    The scripts that I am using are below:

----------------------------
#minimization input file
 &cntrl
        imin = 1,
        maxcyc = 5000, ncyc = 2000, ntmin = 2,
        scee = 1.2,
        nsnb = 25, cut = 8.0,
        ntpr = 100, ntwx = 100, ntwv = 100, ntwe = 100,
        ntb = 0, igb = 1,
        lastist = 7500000, lastrst = 7500000,
 &end

END

----------------------------

----------------------------
#simulated annealing input file
#
#
 &cntrl
    nstlim=22000, pencut=-0.001, nmropt=1,
    ntpr=100, ntt=1, ntwx=200,
    cut=15.0, ntb=0, vlimit=20,
    ntr=1,
    ig=61777,
    lastist = 7500000, lastrst = 7500000,
 /
 &ewald
    eedmeth=5,
 /
 &end
#
 &wt type='TEMP0', istep1=0,istep2=500,value1=0.,
            value2=100., /
 &wt type='TEMP0', istep1=500,istep2=1000,value1=100.,
            value2=100., /
 &wt type='TEMP0', istep1=1001,istep2=1500,value1=100.,
            value2=200., /
 &wt type='TEMP0', istep1=1501,istep2=2000,value1=200.,
            value2=200., /
 &wt type='TEMP0', istep1=2001,istep2=2500,value1=200.,
            value2=300., /
 &wt type='TEMP0', istep1=2501,istep2=3000,value1=300.,
            value2=300., /
 &wt type='TEMP0', istep1=3001,istep2=3750,value1=300.,
            value2=400., /
 &wt type='TEMP0', istep1=3751,istep2=4500,value1=400.,
            value2=400., /
 &wt type='TEMP0', istep1=4501,istep2=5250,value1=400.,
            value2=500., /
 &wt type='TEMP0', istep1=5251,istep2=6000,value1=500.,
            value2=500., /
 &wt type='TEMP0', istep1=6001,istep2=6500,value1=500.,
            value2=550., /
 &wt type='TEMP0', istep1=6501,istep2=9000,value1=550.,
            value2=550., / #
 &wt type='TEMP0', istep1=9001, istep2=11000, value1=550.0,
            value2=450.0, /
 &wt type='TEMP0', istep1=11001, istep2=13000, value1=450.0,
            value2=350.0, /
 &wt type='TEMP0', istep1=13001, istep2=15000, value1=350.0,
            value2=300.0, /
 &wt type='TEMP0', istep1=15001, istep2=22000, value1=300.0,
            value2=300.0, /
 &wt type='TAUTP', istep1=0,istep2=4500,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=4501,istep2=5000,value1=2.0,
            value2=2.0, /
 &wt type='TAUTP', istep1=5001,istep2=9000,value1=2.5,
            value2=3.0, /
 &wt type='TAUTP', istep1=9001,istep2=15000,value1=3.0,
            value2=3.0, /
 &wt type='TAUTP', istep1=15001,istep2=21000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=21001,istep2=22000,value1=0.1,
            value2=0.05, /
 &wt type='END' /
DISANG=dummy
restraint residues1-124
 1.0
RES 1 124
RES 163 292
RES 323 505
RES 575 811
RES 832 1007
END
END
END
END
------------------------

Thanks in advance

-Venkat

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