AMBER Archive (2009)

Subject: [AMBER] Simulated annealing

From: Shaikh Abdul R S Ramaju (smasarsr_at_nus.edu.sg)
Date: Wed Oct 28 2009 - 00:44:33 CDT

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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