In this chapter, I focus on explanatory practices in the field of molecular dynamics (MD) simulations, paying special attention to the role of epistemic strategies—such as abstraction, idealization, and approximation—in the study of biological structures. Specifically, I discuss a particular subclass of idealizations known as defective idealizations. Furthermore, I analyze crucial theoretical and experimental aspects of MD simulations with a particular focus on the class of Gō-like models, highlighting how various epistemic strategies are employed not only in building the model but also in guiding the construction of experimental settings and the conduct of the validation process. On the one hand, I formulate broader philosophical conclusions regarding the explanatory aspects of MD simulations in ensuring scientific understanding of the explanandum, and on the other, I emphasize the limits of mechanistic explanation in this investigative context. Finally, I offer a broader philosophical analysis of the simulation process and demonstrate how my account differs from the “representational bind” and the excessively stringent explanatory strategies of the new mechanists.