The nautilus application was developed to implement the Grid Cell Theory methodology for the spatial resolution of free energies, entropies and enthalpies of water molecules in the vicinity of an organic or a biological molecule . The implementation combined the IO and energy/trajectory analysis functionality of sire to post-process molecular dynamics The FESetup application was developed to automate the preparation of input files for alchemical free energy calculations with a variety of biomolecular simulation packages. FESetup reused sire functionality to parse topologies, and manipulate representations of molecules to generate input files suitable for single-topology alchemical free energy calculations.