This study investigates the impact of timestep on energy drift and free energy calculations, on three chosen molecular systems in various settings. Challenging the current consensus of using a 4 fs timestep with HMR and SHAKE for alchemical free energy calculations, we explore the effects of varying timesteps (0.5-4 fs) on energy drift and dU dλ for the transformation of model systems (cAMP and ethane) as well as well as a protein ligand system (Tyk2 emj 42 to emj 55). NVE simulations demonstrate a clear correlation between increasing timestep and increased energy drift, both with and without HMR. Simulations lacking SHAKE constraints were unstable at larger timesteps. TI simulations in the NPT ensemble, using Langevin dynamics, revealed consistent dU dλ values across 0.5, 1, and 2 fs timesteps. However, significant deviations in dU dλ , reaching up to 3 kcal/mol, were observed at 4 fs in some cases. T-tests confirm statistically significant differences (p < 0.05) between the 4 fs timestep and the 0.5 fs reference, particularly in the aqueous phase. These findings, derived from analysis encompassing various λ states (0-1) and softcore treatments, emphasize the importance of careful timestep selection. We conclude that for accurate and reliable alchemical free energy calculations using HMR and SHAKE, the timestep should be limited to a maximum of 2 fs.