#!/bin/bash

##Should use a different seed for any later
##repeats/extensions of the same calculation.
master_seed=11223355

for system in alphaL alphaR C7ax C7eq
do

  ##use the same set of seeds for
  ##each system, but different seeds
  ##for each lambda
  seed=$master_seed


  ##put each calculation in a separate directory,
  ##just for tidiness
  mkdir -p $system
  cp $system.restraints $system/.
  cd $system
  for lambda in 0.000 0.125 0.250 0.375 0.500 0.625 0.750 0.875 1.000
  do

   seed=$[seed + 17]

   ##prepare the input file with a command-line search-and-replace:
   sed -e "s/_RESTRAINTS_FILE_/$system.restraints/g" \
       -e "s/_SEED_/$seed/g"                         \
       -e "s/_SYS_/$system/"                         \
       -e "s/_LAMBDA_/$lambda/"                      \
       ../md_rest_emil.in > md.$system.$lambda.in

   ##prepare the EMIL input file:
   sed -e "s/_SEED_/$seed/g"                         \
       -e "s/_LAMBDA_/$lambda/"                      \
       ../emilParameters.in > emilParameters.$system.$lambda.in

   ##fork using the `&' operator and launch AMBER:
   nice sander -O -i md.$system.$lambda.in \
                  -p ../diala.top -c ../diala_md1.$system.rst \
                  -o diala_md1.$system.$lambda.out \
                  -x diala_md1.$system.$lambda.x \
                  -r diala_md1.$system.$lambda.rst &


  done
  cd ..
done