  The absolute free energy -- or partition function, equivalently -- of a
molecule can be estimated computationally using a suitable reference system.
Here, we demonstrate a practical method for staging such calculations by
growing a molecule based on a series of fragments. Significant computer time is
saved by pre-calculating fragment configurations and interactions for re-use in
a variety of molecules. We employ such fragment libraries and interaction
tables for amino acids and capping groups to estimate free energies for small
peptides. Equilibrium ensembles for the molecules are generated at no
additional computational cost, and are used to check our results by comparison
to standard dynamics simulation.
