Researchers must go beyond these basics by tailoring their analyses to the unique features of their system. For example, using metadynamics or free energy perturbation methods to explore energy barriers or binding affinities can reveal deeper insights to more appropriately address the research question. Asking specific research questions and developing customized analysis workflows ensures that the simulations produce high-quality, actionable data rather than generic metrics. Additionally, interpreting MD simulation data requires more than presenting raw results-it demands contextualization within the broader biological system. It is not enough to state that a protein has a stable RMSD; researchers must interpret how this "stability," which is really a thermodynamic concept that cannot be derived from RMSD, using several metrics of analysis, affects biological function or interaction. Analyses should support conclusions about biomolecular conformational changes or molecular interactions.