Produce a cpt file every 1 ns for NPT run (for Gromacs ver. 5.1)

run_md-npt.sh

#!/bin/sh

cd ${PBS_O_WORKDIR}
NPROCS=`wc -l <$PBS_NODEFILE`

GMDIR=$HOME/local/gromacs-5.1/bin
GMX=$GMDIR/gmx_d
GROMPP="$GMX grompp"
TPBCONV="$GMX convert-tpr"
MDRUN=$GMDIR/mdrun_mpi_d

TOP=../C4mimNTf2
PREV=eq-npt
STAGE=md-npt

MAXH=1
NPME=-1

# extending 500000 steps per run (= 1ns if timestep is 2fs)
STEP=500000
for i in {0..99}  # run 99 more npt simulations for 99 more .tpr and .cpt file pairs
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
    $TPBCONV -s ${STAGE}-$[i-1].tpr -o ${STAGE}-$i.tpr -nsteps $((STEP * i))
    cp ${STAGE}-$i.tpr ${STAGE}.tpr
    mpirun -n $NPROCS -hostfile $PBS_NODEFILE $MDRUN \
      -deffnm ${STAGE} -cpi ${STAGE} -npme $NPME
    cp ${STAGE}.cpt ${STAGE}-$i.cpt
  fi
done