#!/bin/bash 
#BSUB -P project
#BSUB -J equilibrado
#BSUB -a loadmpi
#BSUB -q q_residual     
#BSUB -n 32
#BSUB -eo err1.err1
#BSUB -oo out1.out1


module purge
module load intel/2015.1.133
module load amber/16
 module load mpi/intel-5.0.2p-044
module load  mpi/openmpi-1.8.3




export AMBERHOME=/opt/SC/amber-16/amber16
 set init = step5_charmm2amber

set cnt = 1
 set cntmax = 5

while [(${cnt} <= ${cntmax} ] 
do
clear
    @ pcnt = ${cnt} - 1

 if ( ${cnt} == 1 ) then
            set pstep = step6.${pcnt}_minimization
            set istep = step6.${cnt}_equilibration
    else
            set pstep = step6.${pcnt}_equilibration
            set istep = step6.${cnt}_equilibration
fi
endif
  mpirun -np 32 sander.MPI  -i ${istep}.mdin -p ${init}.parm7 -c ${pstep}.rst7 -o ${istep}1.mdout -r ${istep}.rst7 -inf ${istep}.mdinfo -ref ${init}.rst7 -x ${istep}.nc

    @ cnt += 1
done