Many-Body Bond Order dissection

1. Load MoleCuilder with the config file to be split up:

   ./molecuilder <PathToConfig>/acetanilide.conf
   

2. Create the Bond Fragments by entering: f 1.55 1. This will look for bonds between atoms at most 1.55 units apart and fragment to first order.
3. Quit MoleCuilder.
4. The config files of the fragments reside in the directory given as the defaultpath in the father config file (must exist).
5. Go to this directory and create all the necessary subdirs with:

   i=0
   while [ -e BondFragment${i}.conf ]; do
     mkdir BondFragment${i}
     let i=$i+1
   done
   

6. Start the simulations ...
7. Use joiner to evaluate total energy and forces in the files pcp.energy.all and pcp.forces.all:

   joiner <PathToConfig>/ pcp