Dear Amber Users,
I am doing simulated annealing for one of the protein. I would like to
analyze at what temperature protein denatures. After initial
minimization, I run simulated annealing for 250 ps. Following are the
input parameters used in simulated annealing. I found that temperature
increases up to 300 K and after that it remains constant with minor
fluctuations. Can somebody help me to solve this problem. Please have a
look on following input file.
Thanks a lot
Regards
Abdul Rajjak
**********simulated annealing protocol, ******
&cntrl
imin=0, irest=0, ntx=1,
ntc=1, ntf=1,
ntpr=500, ntwx=10000
ntb=0, cut=16.0, rgbmax=15.0,
igb=1, saltcon=0.2,
nstlim=500000, nscm=0,
dt=0.0005, scee=1.2,
ntt=1,
/
&ewald
eedmeth=5,
/
#
#Simple simulated annealing algorithm:
#
#from steps 0 to 100000: heat the system from 10 to 300K
#from steps 100001 to 150000: maintain at 300K
#from steps 150001 to 250000: heat the system till 400K
#from steps 250001 to 300000: maintain at 400K
#from steps 300001-400000: re-cool to 300 K
#from steps 400001 to 500000: equilibrate at 300 K
#
&wt type='TEMP0', istep1=0,istep2=100000,
value1=10.0, value2=300.0
/
&wt type='TEMP0', istep1=100001,istep2=150000,
value1=300.0, value2=300.0
/
&wt type='TEMP0', istep1=150001, istep2=250000,
value1=300.0, value2=400.0
/
&wt type='TEMP0', istep1=250001, istep2=300000,
value1=400.0, value2=400.0
/
&wt type='TEMP0', istep1=300001, istep2=400000,
value1=400.0, value2=300.0
/
&wt type='TEMP0', istep1=400001, istep2=500000,
value1=300.0, value2=300.0
/
&wt type='TAUTP', istep1=0,istep2=100000,
value1=0.2, value2=0.2
/
&wt type='TAUTP', istep1=100001,istep2=150000,
value1=1.0, value2=1.0
/
&wt type='TAUTP', istep1=150001,istep2=250000,
value1=0.2, value2=0.2
/
&wt type='TAUTP', istep1=250001,istep2=300000,
value1=0.2, value2=0.2
/
&wt type='TAUTP', istep1=300001, istep2=400000,
value1=0.2, value2=0.2,
/
&wt type='TAUTP', istep1=400001, istep2=500000,
value1=1.0, value2=1.0,
/
&wt type='END'
/
END
END
************************************
Dr. Shaikh Abdul Rajjak,
Research Fellow
Singapore-MIT Alliance
National University of Singapore
Singapore 117576
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Received on Tue Oct 27 2009 - 23:00:02 PDT
