A central observation from this work is the marked increase in energy drift with larger timesteps across all systems studied (Tables ). For the cAMP system with SHAKE and HMR enabled, energy drift increased by 318% when moving from 0.5 fs to 4 fs timesteps, while the ethane system showed a staggering 10,000% (two orders of magnitudes) increase under comparable conditions. This nonlinear relationship between timestep size and energy conservation violations suggests that traditional stability metrics may insufficiently capture the subtle thermodynamic perturbations induced by temporal discretization. Particularly concerning was the instability observed in simulations lacking SHAKE constraints at timesteps ≥ 2 fs, emphasizing the algorithm's critical role in maintaining numerical stability during alchemical transformations.