#!/bin/bash

for system in alphaL alphaR C7ax C7eq
do

   ##prepare the input file with a command-line search-and-replace:
   sed -e "s/_RESTRAINTS_FILE_/$system.restraints/g" \
       md1ns_rest.template.in > md_rest.$system.in

   ##fork using the `&' operator and launch sander (or pmemd):
   nice sander -O -i md_rest.$system.in \
                  -p diala.top -c diala.crd \
                  -o diala_md1.$system.out \
                  -x diala_md1.$system.x \
                  -r diala_md1.$system.rst &
done