AMBER Archive (2002)

Subject: Fw: amber problem

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Wed Aug 28 2002 - 12:10:26 CDT

I am forwarding this to the AMBER mailing list.
That is where you should send these questions, so
all AMBER users can try to help.
Carlos

> Dr. Bill told me that I should read the FAQ about
> equilibration. And I searched some input template in the netscape, and
> found a simulated annealing could solve my problem, the sander does not
> stop. But in the output file, it always says that "vlimit exceeded for
> step *; vmax = 39.8214423", or something like that. So I wonder if it
> would influence my results.
> Another question about sander is, I am confused about when I
> should use the ntb=1, and ntb=2. My protein is soaked in a cubic water
> box. To make PBC work, which parameter should I use. My new input file
> is the following, I have changed some parameters, I wish you could tell
> me if there are something wrong in it.
> Thank you very much for your advice.
>
> --------------------------------
> &cntrl
> nstlim=20000,
> ntpr=200, ntt=1, ntwx=200,
> ntb=1, vlimit=20,scee=1.2,
> &end
> &ewald
> eedmeth=5,
> &end
> #
> #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., &end
> &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
> value2=100.0, &end
> &wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
> value2=0.0, &end
>
> &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
> value2=0.4, &end
> &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
> value2=4.0, &end
> &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
> value2=1.0, &end
> &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
> value2=0.05, &end
>
> &wt type='REST', istep1=0,istep2=3000,value1=0.1,
> value2=1.0, &end
> &wt type='REST', istep1=3001,istep2=20000,value1=1.0,
> value2=1.0, &end
>
> &wt type='END' &end
> --------------------------------
>
>