Explanation is commonly considered one of the central goals of science. Although computer simulations have become an important tool in many scientific areas, various philosophical concerns indicate that their explanatory power requires further scrutiny. We examine a case study in which atomistic simulations have been used to examine the factors responsible for the transport selectivity of certain channel proteins located at cell membranes. By elucidating how precisely atomistic simulations helped scientists draw inferences about the molecular system under investigation, we respond to some concerns regarding their explanatory power. We argue that atomistic simulations can be tools for managing molecular complexity and for systematically assessing how the occurrence of the explanandum is sensitive to a range of factors.