Produce a cpt file every 1 ns for NPT run (for Gromacs ver. 4)

run_md-npt.sh

#PBS -l nodes=2:ppn=12
#PBS -N JobName

cd ${PBS_O_WORKDIR}
NPROCS=`wc -l <$PBS_NODEFILE`
MPIRUN="mpirun -machinefile $PBS_NODEFILE -n $NPROC"

export GMX_MAXBACKUP=1000  # max number of gro backup

GMDIR=/home/kmtu/local/gromacs-4.6.6/bin
GROMPP=$GMDIR/grompp_d
MDRUN=$GMDIR/mdrun_mpi_d
TPBCONV=$GMDIR/tpbconv_d

PREV=eq-npt2  # name of the previous stage
STAGE=md-npt  # name of the current stage
TOP=../system  # topology file (without the .top extension)
TIME=1000  # extending 1000 ps (1 ns) per run

for i in {0..9}
do
  if [ $i == 0 ]; then
    ln -s $PREV.cpt ${STAGE}-$i.cpt
    $GROMPP -f $STAGE.mdp -c $PREV.tpr -p $TOP.top -o ${STAGE}-$i.tpr -t $PREV.cpt
  else
    if [ $i == 1 ]; then
      $TPBCONV -s ${STAGE}-$[i-1].tpr -o ${STAGE}-$i.tpr -until ${TIME}
    else
      $TPBCONV -s ${STAGE}-$[i-1].tpr -o ${STAGE}-$i.tpr -extend ${TIME}
    fi
    cp ${STAGE}-$i.tpr ${STAGE}.tpr
    $MPIRUN $MDRUN -deffnm ${STAGE} -cpi ${STAGE}
    cp ${STAGE}.cpt ${STAGE}-$i.cpt
  fi
done