AMBER Archive (2002)

Subject: question on ouput of sander

From: Sichun Yang (syang_at_physics.ucsd.edu)
Date: Mon Oct 21 2002 - 13:19:17 CDT

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