Fragmenting Molecules

In the following we use molecuilder to generate all possible fragments of a given molecule:

./molecuilder -i <input> -I --fragment-molecule ./ --distance 2. --order 4

which takes the file <input>, creates the bond graph (--I), and fragments the molecule up to order 4 (--order).

This will create files BondFragment###.conf (and with .in suffix, too) in the current (./) directory where ### starts at 0 and counts through all created fragments.

These can subsequently be used with PCP or MPQC to calculate the fragment energy.