View source for With t4 step2 min.bash

 #!/bin/bash
 wd=`pwd`
 pre0='t4_bnz'
 pre1='t4_phn'
 mask0=':BNZ@H6'
 mask1=':PHN@O1,H6'
 
 for X in 1 2 3 4 5 6 7 8 9
 
 do
 
 cat << EOF > group_min_l${X}
 -O -i mdin_min_v0_l${X} -o ${pre0}_min_v0_l${X}.out -p ../${pre0}.prm -c ../${pre0}.rst -r ${pre0}_min_v0_l${X}.rst
 -O -i mdin_min_v1_l${X} -o ${pre1}_min_v1_l${X}.out -p ../${pre1}.prm -c ../${pre1}.rst -r ${pre1}_min_v1_l${X}.rst
 EOF
 
 cat << EOF > mdin_min_v0_l${X}
 density minlibration
  &cntrl
   imin = 1, ntx=1, 	
   maxcyc=500,
   ntmin=2,
   ntpr = 100,
   ntf = 1,      ntc = 1,
   ntb = 1,	cut = 9.0,
   icfe=1,	clambda = 0.${X},
 EOF
 
 cp mdin_min_v0_l${X} mdin_min_v1_l${X}
 
 cat << EOF >> mdin_min_v0_l${X}
   ifsc=1,
   crgmask='${mask0}',
   scmask='${mask0}',
  &end
 EOF
 cat << EOF >> mdin_min_v1_l${X}
   ifsc=1,
   crgmask='${mask1}',
   scmask='${mask1}',
  &end
 EOF
 
 sander="${AMBERHOME}/exe/sander.MPI"
 cd $wd
 rm -rf zzz.minqsub.out.${X} zzz.minqsub.err.${X} minrun.pbs.${X}
 
 cat << EOF > minrun.pbs.${X}
 #!/bin/bash
 #PBS -l nodes=1:ppn=2
 #PBS -l walltime=168:00:00
 #PBS -o zzz.minqsub.out.${X}
 #PBS -e zzz.minqsub.err.${X}
 
 cd $wd
 cat \$PBS_NODEFILE | sort | uniq > mpd.nodes.${X}
 
 mpdboot --totalnum=-1 --ncpus=2 -f mpd.nodes.${X}
 mpiexec -n 2 $sander -O -ng 2 -groupfile group_min_l${X}
 
 mpdallexit
 EOF
 
 chmod +x minrun.pbs.${X}
 qsub minrun.pbs.${X}
 
 done