[AMBER] Error in Sander Output File

From: Alison Saunders <alison.m.saunders.gmail.com>
Date: Tue, 28 Jul 2009 18:00:12 +0100

*Hello,

I am having a problem with the output files from sander. I first minimized
the system, heated it up to about 300 K, and then ran the following script:*

#!/bin/sh
#$ -S /bin/bash
#$ -cwd
#$ -j y
#$ -M
#$ -m beas
#$ -N Production
#$ -e sge.err
#$ -o sqe.out

# This script is for parallel AMBER9 production runs on
Tribe.cse.ucdavis.edu

protein=CPEBQ1
out=$protein.out

# Load the required modules
module load compilers/pathscale-3.2 \
        blas/acml-4.1.0-pathscale \
        mpi/openmpi-1.2.6-pathscale-3.2 \
        md/amber-9-pathscale

# Run Sander: sander [-O] -i mdin -o mdout -p prmtop -c inpcrd
# -r restrt [-ref refc] [-x mdcrd] [-v mdvel] [-e mden] [-inf mdinfo]
mpirun -v sander.MPI -O \
        -i Isobaric10ns.in \
        -o $out/Isobaric10ns.out \
        -p $protein.prmtop \
        -c $out/Isochoric4.rst \
        -r $out/Isobaric10ns.rst \
        -x $out/Isobaric10ns.mdcrd < /dev/null
gzip -q $out/Isobaric10ns.mdcrd



*The output file looks normal up to a certain point where it shows only .
signs. It then continues normally:
*
 NSTEP = 920000 TIME(PS) = 1860.000 TEMP(K) = 298.98 PRESS =
-272.1
 Etot = -24453.6029 EKtot = 5817.8174 EPtot =
-30271.4203
 BOND = 163.5141 ANGLE = 460.5464 DIHED =
633.5620
 1-4 NB = 195.7649 1-4 EEL = 2237.3829 VDWAALS =
3569.4836
 EELEC = -37531.6742 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 2583.3338 VIRIAL = 3144.1892 VOLUME =
95475.0654
                                                    Density =
1.0209
 Ewald error estimate: 0.1817E-03
 ------------------------------------------------------------------------------


 NSTEP = 930000 TIME(PS) = 1880.000 TEMP(K) = 295.67 PRESS =
220.1
 Etot = -24357.4522 EKtot = 5753.3771 EPtot =
-30110.8293
 BOND = 192.6911 ANGLE = 471.5489 DIHED =
656.3738
 1-4 NB = 197.3887 1-4 EEL = 2214.4488 VDWAALS =
3567.3524
 EELEC = -37410.6330 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT =
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
........
.........
.........
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
^.^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
 NSTEP = 1110000 TIME(PS) = 2240.000 TEMP(K) = 295.79 PRESS =
116.3
 Etot = -24441.2541 EKtot = 5755.6413 EPtot =
-30196.8954
 BOND = 197.1752 ANGLE = 469.5430 DIHED =
642.9165
 1-4 NB = 191.8450 1-4 EEL = 2216.4663 VDWAALS =
3651.9171
 EELEC = -37566.7585 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 2570.3827 VIRIAL = 2330.7991 VOLUME =
95388.6909
                                                    Density =
1.0219
 Ewald error estimate: 0.2058E-03
 ------------------------------------------------------------------------------


*Do you have any idea what is going on here? Thanks!
Alison Saunders*
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Received on Tue Jul 28 2009 - 10:11:02 PDT
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