AMBER Archive (2009)

Subject: Re: [AMBER] Simulated annealing

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Oct 28 2009 - 05:51:41 CDT

without setting nmropt=1 the temperature change section will not be read.

it's always a good idea to look at your output file and see if sander
understood what you wanted it to do. if you ask for a temperature change (or
other weight change), it will describe this before it starts writing the
energies. in your case it probably never says anything about temperature
change- which means it didn't read those commands.

there are other things wrong as well- for example, the &ewald section is not
read is you are using igb>0.
you can't mix GB and PME.

in general I don't think this simulation will be that informative. igb=1 is
known to be a poor solvent model, and in 250ps your protein is unlikely to
unfold (just too short). to really understand denaturation temperature you
would need a much more complex simulation (or set of them) that equilibrates
at multuple temperatures. remember that proteins unfold at all temperatures-
it's just a question of the unfolding rate vs folding rate and how each
depends on temperature, and these are both statistical measures that cannot
be described well by observing a single event.

On Wed, Oct 28, 2009 at 1:44 AM, Shaikh Abdul R S Ramaju <
smasarsr_at_nus.edu.sg> wrote:

> 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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>
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