Having set up the computational workflow, and confirmed that single point energies of molecular systems are consistent between SOMD and OpenMM, we turn now to validation of free energies using the QUBE/Sire molecular system. A recent investigation of the reproducibility of (relative and absolute) hydration free energy calculations across contemporary molecular simulation packages (including SOMD and GROMACS) has provided benchmarks and package-specific protocols that serve as a validation test of new free energy procedures. Using the same benchmark test set used in this previous study, we therefore test the agreement between absolute hydration free energies computed using the QUBE force field, as implemented in GROMACS and our new Sire interface. Small molecule input files were prepared using QUBEKit and Sire in the same way as the NNRTI compounds (Computational Methods). GROMACS force field files were generated from the corresponding AM-BER input files using BioSimSpace. Free energy protocols were as previously described (Supporting Methods) and a tutorial is provided (SOMD-paper/tree/main/HFE). Figure compares the absolute hydration free energies for nine molecules, computed using SOMD and GROMACS. The mean absolute deviation in the computed hydration free energies is 0.15 kcal/mol which is consistent with the level of reproducibility reported between other packages. Thus we can be confident of our implementation of QUBE in the Sire molecular simulation framework.