In molecular dynamics (MD) simulations, an equilibration phase is used to bring the system to the desired conditions (e.g. temperature and pressure) before collecting data in more extensive production phases. Ideally, the equilibration phase would bring the system to the correct equilibrium ensemble appropriate for the target thermodynamic conditions. Many studies give relatively little attention to details of the equilibration protocol as long as the system eventually reaches stabilization at the correct temperature, pressure, volume, etc. However, in a previous study we found a surprising instability of two ligands in a binding site. That led us to study the origin of this instability more, and in the present work we have traced it to details of the equilibration protocol. We found for the studied system, different equilibration schemes caused dramatic differences in sampled configurations of the system in production runs, highlighting the importance of careful consideration of equilibration schemes in MD simulations.