AMBER Archive (2002)

Subject: Re: question on ouput of sander

From: Sichun Yang (syang_at_physics.ucsd.edu)
Date: Mon Oct 21 2002 - 13:45:29 CDT

I have got my first question.
Thanks!

> Dear All,
>
> I have a question about my output.
> The input shows below.
> But I can get all the ouput files but the -x sa.crd and -e sa.en.
> Any suggestion?
>
> By the way, I get an error from the mdinfo file
> Ewald error estimate: 0.1000E+01
> What do this mean?
>
> Thank you in advance.
>
>
> MY INPUT:
> cat <<eof >sa.in
> #
> simulated annealing
> #
> &cntrl
> imin=0,nmropt=1,
> irest=0,
> ntpr=500,
> ntb=0, cut=12.0,
> nstlim=15000,
> ntt=1, tempi=0.0, temp0=300.0, vlimit=20,
> &end
> #
> # Simple simulated annealing algorithm:
> #
> &wt type='TEMP0', istep1=0,istep2=1000,value1=10.,
> &wt type='TEMP0', istep1=0,istep2=1000,value1=10.,
> value2=400., &end
> &wt type='TEMP0', istep1=1001, istep2=3000, value1=400.,
> value2=400.0, &end
> &wt type='TEMP0', istep1=3001, istep2=15000, value1=0.,
> value2=0.0, &end
> #
> # Strength of temperature coupling:
> #
> &wt type='TAUTP', istep1=0,istep2=3000,value1=0.2,
> value2=0.2, &end
> &wt type='TAUTP', istep1=3001,istep2=11000,value1=4.0,
> value2=2.0, &end
> &wt type='TAUTP', istep1=11001,istep2=13000,value1=1.0,
> value2=1.0, &end
> &wt type='TAUTP', istep1=13001,istep2=14000,value1=0.5,
> value2=0.5, &end
> &wt type='TAUTP', istep1=14001,istep2=15000,value1=0.05,
> value2=0.05, &end
> #
> # "Ramp up" the restraints over the first 3000 steps:
> #
> &wt type='REST', istep1=0,istep2=3000,value1=0.1,
> &wt type='TAUTP', istep1=13001,istep2=14000,value1=0.5,
> value2=0.5, &end
> &wt type='TAUTP', istep1=14001,istep2=15000,value1=0.05,
> value2=0.05, &end
> #
> # "Ramp up" the restraints over the first 3000 steps:
> #
> &wt type='REST', istep1=0,istep2=3000,value1=0.1,
> value2=1.0, &end
> &wt type='REST', istep1=3001,istep2=15000,value1=1.0,
> value2=1.0, &end
> &wt type='END' &end
> LISTOUT=POUT
> DISANG=dummy
> eof
>
> /sander -O -i sa.in \
> -o sa.out \
> -p prmtop.sh3 \
> -c min1.crd \
> -e sa.en \
> -r restrt.crd \
> -x sa.crd
>
>
>