Overall, we have demonstrated that conformer dependent charge assignment methods can have a functionally important e ect on calculated absolute hydration free energy values with ranges of up to 6.9 ± 0.1 kcal/mol from only input conformer di erences. Using the same input conformer and charge assignment methods but di erent hardware can result in calculated absolute hydration free energy values with ranges of up to 3.8±0.1 kcal/mol. This means that binding free energy studies, which have even more degrees of freedom and sources of variability, will su er from unpredictable performance introduced by variation in partial charge set. These results thus highlight the importance of using reproducible partial charges that are relevant to the problems or questions we are trying to address in our simulations.