There are many available open-source MD engines to run massively parallel simulations, each of which come with their own considerations, quirks, and best practices. In this section, we will outline popular open-source MD engines worth considering for running massively parallel MD simulations, as well as the best ways to run them. Given the existing variance in software implementations between engines, the results from one software may not easily be transferable or comparable to MD simulation frames from another engine. One should use caution when trying to compare simulation results collected using different engines, as minor differences between the implementations can lead to large changes in ensemble properties due to the high Lyapunov exponent (the rate of divergence between two trajectories that have only slightly different starting conditions) of biomolecular MD simulations .