AMBER Archive (2004)

Subject: Re: AMBER: simulated anealling

From: Rhonda Torres (
Date: Thu Jun 03 2004 - 13:05:58 CDT

Hi Anshul,

You mention that you used a variation of your file given below (the
the group information apparently at the end of the file). Also from
what you have provided, it appears that the restraint information is
not being read in. You should have a LISTOUT=POUT type statement
which gets the restraint violation list and a DISTANG=RST.f statement
that reads in the file containing your actual restraints.

Could you please send the input file you are currently using to attempt
this simulation as it will allow us to better help you solve the problem.

I don't know why you want to include group restraints in your
simulated annealing simulation, but I would recommend you first attempt a
simulation without the group restraint information, following the
procedure outlined in the NMR refinement of a DNA duplex tutorial.


 simulated annealing protocol, 20 ps

    nstlim=20000, pencut=-0.001, nmropt=1,
    ntpr=200, ntt=1, ntwx=200,
    cut=15.0, ntb=0, vlimit=10,
#Simple simulated annealing algorithm:
#from steps 0 to 5000: heat the system to 600K
#from steps 5001-18000: re-cool to low temperatures with long tautp
#from steps 18001-20000: final cooling with short tautp
 &wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
            value2=600., /
 &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
            value2=100.0, /
 &wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
            value2=0.0, /

 &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
            value2=0.4, /
 &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
            value2=4.0, /
 &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
            value2=0.05, /

 &wt type='REST', istep1=0,istep2=3000,value1=0.1,
            value2=1.0, /
 &wt type='REST', istep1=3001,istep2=20000,value1=1.0,
            value2=1.0, /

 &wt type='END' /


Hope this helps......Rhonda

On Thu, 3 Jun 2004 wrote:

> Hi all,
> I am trying to do simulated anealling and had written earlier also about
> the problems i faced in the same process. Previously I was told by Dac
> that I should place the group information regarding the restraints after
> the cntrl section but I was not able to run the process properly as the
> groups were not read. So itried to run the same process by keeping the
> group information in the begining followed by cntrl section and then
> eedmeth=5 flag. this time it is running fine.
> 1 it reads the group nformation properly
> 2. sets the dielectric to distance dependent
> i want to know if this is all right or not. Any comments regarding
> theis process will be helpful. Here is my input file for the
> same process
> Group input for restrained atoms (A1-A166)
> 2
> RES 1 167 END
> Group input for restrained atoms (A182-A276)
> 2
> RES 182 276
> &cntrl
> imin=0, cut=30, nstlim=90000, ntt=1, ntx=1, irest=0,
> ntpr=500, ntwx=500, ntwe=500, tempi=10,
> ntb=0, ntr=1, dielc=4, vlimit=30, nmropt=1,
> &end
> &ewald
> eedmeth=5,
> &end
> &wt type='TEMP0', istep1=0,istep2=50000,value1=10.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=50001,istep2=60000,value1=500.0,
> value2=500.0, &end
> &wt type='TEMP0', istep1=60001,istep2=70000,value1=500.0,
> value2=300.0, &end
> &wt type='TEMP0', istep1=70001,istep2=90000,value1=300.0,
> value2=300.0, &end
> &wt type='TAUTP', istep1=0,istep2=50000,value1=1.0,
> value2=1.0 &end
> &wt type='TAUTP', istep1=50001,istep2=60000,value1=0.5,
> value2=0.5, &end
> &wt type='TAUTP', istep1=60001,istep2=70000,value1=0.5,
> value2=0.5 &end
> &wt type='TAUTP', istep1=70001,istep2=90000,value1=0.2,
> value2=0.2 &end
> &wt type='END' &end
> With regards,
> Anshul
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