View source for With t4 step3 inputgen.bash

 #!/bin/bash
 wd=`pwd`
 pre0='t4_phn'
 pre1='t4_phn'
 mask0=':PHN@O1,H6'
 mask1=''
 
 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 > group_equi_l${X}
 -O -i mdin_equi_v0_l${X} -o ${pre0}_equi_v0_l${X}.out -p ../${pre0}.prm -c ${pre0}_min_v0_l${X}.rst -r ${pre0}_equi_v0_l${X}.rst
 -O -i mdin_equi_v1_l${X} -o ${pre1}_equi_v1_l${X}.out -p ../${pre1}.prm -c ${pre1}_min_v1_l${X}.rst -r ${pre1}_equi_v1_l${X}.rst
 EOF
 cat << EOF > group_prod_l${X}
 -O -i mdin_prod_v0_l${X} -o ${pre0}_prod_v0_l${X}.out -p ../${pre0}.prm -c ${pre0}_equi_v0_l${X}.rst -r ${pre0}_prod_v0_l${X}.rst -x ${pre0}_prod_v0_l${X}.crd
 -O -i mdin_prod_v1_l${X} -o ${pre1}_prod_v1_l${X}.out -p ../${pre1}.prm -c ${pre1}_equi_v1_l${X}.rst -r ${pre1}_prod_v1_l${X}.rst -x ${pre1}_prod_v1_l${X}.crd
 EOF
 
 cat << EOF > mdin_min_v0_l${X}
 density minlibration
  &cntrl
   imin = 1,	ntx = 1,
   maxcyc=500,
   ntpr = 100,
   ntf = 2,      ntc = 2,
   ntb = 1,	cut = 9.0,
   icfe=1,	clambda = 0.${X},
 EOF
 
 cp mdin_min_v0_l${X} mdin_min_v1_l${X}
 
 cat << EOF >> mdin_min_v0_l${X}
   ifsc=0,
   crgmask='${mask0}',
  &end
 EOF
 cat << EOF >> mdin_min_v1_l${X}
   ifsc=0,
   crgmask='${mask1}',
  &end
 EOF
 
 cat << EOF > mdin_equi_v0_l${X}
 density equilibration
  &cntrl
   imin = 0,	ntx = 1,	irest = 0,
   ntpr = 2500,	ntwr = 10000,	ntwx = 0,
   ntf = 2,      ntc = 2,
   ntb = 2,	cut = 9.0,
   nstlim = 25000,	dt = 0.002,
   temp0 = 300.0,	ntt = 3,	gamma_ln = 5,
   ntp = 1,	pres0 = 1.0,	taup = 0.2,
   icfe=1,	clambda = 0.${X},
 EOF
 
 cp mdin_equi_v0_l${X} mdin_equi_v1_l${X}
 
 cat << EOF >> mdin_equi_v0_l${X}
   ifsc=0,
   crgmask='${mask0}',
  &end
 EOF
 cat << EOF >> mdin_equi_v1_l${X}
   ifsc=0,
   crgmask='${mask1}',
  &end
 EOF
 
 cat << EOF > mdin_prod_v0_l${X}
 NPT production
  &cntrl
   imin = 0,	ntx = 5,	irest = 1,
   ntpr = 10000,	ntwr = 100000,	ntwx = 10000,
   ntf = 2,	ntc = 2,
   ntb = 2,	cut = 9.0,
   nstlim = 100000,	dt = 0.002,
   temp0 = 300.0,	ntt = 3,	gamma_ln = 2,
   ntp = 1,	pres0 = 1.0,	taup = 2.0,
   icfe=1,       clambda = 0.${X},
 EOF
 
 cp mdin_prod_v0_l${X} mdin_prod_v1_l${X}
 
 cat << EOF >> mdin_prod_v0_l${X}
   ifsc=0,
   crgmask='${mask0}',
  &end
 EOF
 cat << EOF >> mdin_prod_v1_l${X}
   ifsc=0,
   crgmask='${mask1}',
  &end
 EOF
 
 sander="${AMBERHOME}/exe/sander.MPI"
 cd $wd
 rm -rf zzz.qsub.out.${X} zzz.qsub.err.${X} run.pbs.${X}
 
 cat << EOF > run.pbs.${X}
 #!/bin/bash
 #PBS -l nodes=2:ppn=2
 #PBS -l walltime=72:00:00
 #PBS -o zzz.qsub.out.${X}
 #PBS -e zzz.qsub.err.${X}
 
 cd $wd
 cat \$PBS_NODEFILE | sort | uniq > mpd.nodes.${X}
 
 mpdboot --totalnum=-1 --ncpus=2 -f mpd.nodes.${X}
 mpiexec -n 4 $sander -O -ng 2 -groupfile group_min_l${X}
 mpiexec -n 4 $sander -O -ng 2 -groupfile group_equi_l${X}
 mpiexec -n 4 $sander -O -ng 2 -groupfile group_prod_l${X}
 
 mpdallexit
 EOF
 
 chmod +x run.pbs.${X}
 qsub run.pbs.${X}
 
 done