AMBER Archive (2009)

Subject: [AMBER] Simulated annealing

From: waleed zalloum (waleed_zalloum_at_yahoo.com)
Date: Thu Oct 15 2009 - 05:59:29 CDT

Dear Amber users,
 
I am calculating a 3D structure of a oligopeptide conjugated to single stranded DNA. I run NMR restrained simulated annealing. I specified certain heat range for certain number of steps ( as in the input file bellow). Upon running,  the heat does not stick to the  specified  number of steps and there is a huge fluctuation in the temperature (eg. from 600 going to 800 and then go back to 650). What is the problem? is there any problem in the input file?
 
I specified the LISTOUT option, but I don't get any output list coming after the end of simulation? what is the problem in that?
 
ps. Bellow is the annealing input file.
 
Thank you

  
 
Waleed
                                                                             
 &cntrl                                                                       
    nstlim=190000, pencut=-0.001, nmropt=1,ipnlty=1,scee=1.2,
    ntpr=200, ntt=3, ntwx=200,imin=0,gamma_ln=1.0,irest=0,ntx=1,
    cut=9.0, ntb=0, vlimit=10, dt=0.001, igb=1, ntc=2, ntf=2,temp0=500
 /                                                                       
 &ewald
    eedmeth=5,
 /
#                                                                              
                                                                              
 &wt type='TEMP0', istep1=0,istep2=2000,value1=500.0,
            value2=500.0,    /
 &wt type='TEMP0', istep1=2001, istep2=5000, value1=500.0,
            value2=1000.0,     /
 &wt type='TEMP0', istep1=5001, istep2=10000, value1=1000.0,
            value2=1000.0,     /
 &wt type='TEMP0', istep1=10001, istep2=20000.0, value1=1000.0,
            value2=950.0,     /
 &wt type='TEMP0', istep1=20001, istep2=30000.0, value1=950.0,
            value2=900.0,     /
 &wt type='TEMP0', istep1=30001, istep2=40000.0, value1=900.0,
            value2=850.0,     /
 &wt type='TEMP0', istep1=40001, istep2=50000, value1=850.0,
            value2=800.0,     /
 &wt type='TEMP0', istep1=50001, istep2=60000, value1=800.0,
            value2=750.0,     /
 &wt type='TEMP0', istep1=60001, istep2=70000, value1=750.0,
            value2=700.0,     /
 &wt type='TEMP0', istep1=70001, istep2=80000, value1=700.0,
            value2=650.0,     /
 &wt type='TEMP0', istep1=80001, istep2=90000, value1=650.0,
            value2=600.0,     /
 &wt type='TEMP0', istep1=90001, istep2=100000, value1=600.0,
            value2=550.0,     /
 &wt type='TEMP0', istep1=100001, istep2=110000, value1=550.0,
            value2=500.0,     /
 &wt type='TEMP0', istep1=110001, istep2=120000, value1=500.0,
            value2=450.0,     /
 &wt type='TEMP0', istep1=120001, istep2=130000, value1=450.0,
            value2=400.0,     /
 &wt type='TEMP0', istep1=130001, istep2=140000, value1=400.0,
            value2=350.0,     /
 &wt type='TEMP0', istep1=140001, istep2=150000, value1=350.0,
            value2=300.0,     /
 &wt type='TEMP0', istep1=150001, istep2=160000, value1=300.0,
            value2=250.0,     /
 &wt type='TEMP0', istep1=160001, istep2=170000, value1=250.0,
            value2=200.0,     /
&wt type='TEMP0', istep1=170001, istep2=180000, value1=200.0,
            value2=150.0,     /
&wt type='TEMP0', istep1=180001, istep2=190000, value1=150.0,
            value2=100.0,     /
 

 &wt type='TAUTP', istep1=0,istep2=10000,value1=0.4,
            value2=0.4,     /
 &wt type='TAUTP', istep1=10001,istep2=170000,value1=4.0,
            value2=4.0,     /
 &wt type='TAUTP', istep1=170001,istep2=180000,value1=1.0,
            value2=1.0,     /
 &wt type='TAUTP', istep1=180001,istep2=190000,value1=0.1,
            value2=0.1,     /                   
                           
 &wt type='REST', istep1=0,istep2=5000,value1=0.0,                            
            value2=0.0,  /                                               
 &wt type='REST', istep1=5001,istep2=10000,value1=0.0,                       
            value2=0.01,   /
 &wt type='REST', istep1=10001,istep2=20000,value1=0.01,
            value2=0.1,  /
 &wt type='REST', istep1=20001,istep2=30001,value1=0.1,
            value2=0.15,  /
 &wt type='REST', istep1=30001,istep2=40000,value1=0.15,
            value2=0.2,  /
 &wt type='REST', istep1=40001,istep2=50000,value1=0.2,
            value2=0.25,  /
 &wt type='REST', istep1=50001,istep2=60000,value1=0.25,
            value2=0.3,  /
 &wt type='REST', istep1=60001,istep2=100000,value1=0.3,
            value2=0.6,  /
 &wt type='REST', istep1=100001,istep2=150000,value1=0.6,
            value2=0.9,  /
 &wt type='REST', istep1=150001,istep2=190000,value1=0.9,
            value2=1.0,  /                                             
                                                                              
 &wt type='END'  /
LISTOUT=POUT                                                                  
DISANG=RST       

 

 

      
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