Dear All,
I tried to run some simulation annealing on a complex of a protein and
DNA, with Langevin thermobath and igb=1. I have trouble to understand
the function of nscm. If nscm=0, the temperature is well controlled. But
if nscm=500 or 1000, as suggested by a tutorial, the temperature looks
very strange (at some points it goes uo to 1000K, see my following input
file). I do not know why nscm needs to set and how it effects the
temperature. I am learning AMBER slowly. Any help is highly appreciated.
Following is my input file:
> 300ps kuc DNA simulated annealing
> &cntrl
> imin = 0, irest = 0,
> ntc=1, ntf=1,
> ntpr=500, ntwx=1000,
> ntb = 0, cut = 12.0, rgbmax=12.0,
> igb = 1, saltcon=0.2,
> nstlim = 600000, nscm= 500,
> dt = 0.0005,
> ntt = 3, gamma_ln=1.0,
> temp0=300,
> nmropt=1,ntr=1
> /
> &wt type='TEMP0', istep1=0,istep2=100000,
> value1=0.0, value2=300.0
> /
> &wt type='TEMP0', istep1=100001,istep2=200000,
> value1=300.0, value2=400.0
> /
> &wt type='TEMP0', istep1=200001,istep2=300000,
> value1=400.0, value2=500.0
> /
> &wt type='TEMP0', istep1=300001,istep2=400000,
> value1=500.0, value2=500.0
> /
> &wt type='TEMP0', istep1=400001,istep2=500000,
> value1=500.0, value2=300.0
> /
> &wt type='TEMP0', istep1=500001,istep2=600000,
> value1=300.0, value2=300.0
> /
>
> &wt type='REST', istep1=0,istep2=300000,value1=0.1,
> value2=0.75 /
> &wt type='REST', istep1=300001,istep2=600000,value1=1.0,
> value2=1.0, /
>
> &wt type='END'
> /
> LISTOUT=POUT
> DISANG=RST
> Hold the protein fixed
> 5.0
> RES 21 74
> END
> END
Thanks in advance,
Shaowen
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Received on Sun Apr 15 2007 - 06:07:21 PDT
