Ion channels are implicated in many essential physiological events such as electrical signal propagation and cellular communication. The advent of K+ and Na+ ion channel structure determination has facilitated numerous investigations of molecular determinants of their behaviour. At the same time, rapid development of computer hardware and molecular simulation methodologies has made computational studies of large biological molecules in all‐atom representation tractable. The concurrent evolution of experimental structural biology with biomolecular computer modelling has yielded mechanistic details of fundamental processes unavailable through experiments alone, such as ion conduction and ion channel gating. This review is a short survey of the atomistic computational investigations of K+ and Na+ ion channels, focusing on KcsA and several voltage‐gated channels from the KV and NaV families, which have garnered many successes and engendered several long‐standing controversies regarding the nature of their structure–function relationship. We review the latest advancements and challenges facing the field of molecular modelling and simulation regarding the structural and energetic determinants of ion channel function and their agreement with experimental observations.  Structural illustration of the voltage‐gated potassium channel gating transitions studied by atomistic molecular dynamics simulations including voltage‐dependent activation/deactivation associated with channel pore opening and closing and voltage sensor domain (VSD) movement as well as C‐type inactivation processes associated with selectivity filter distortions. A single file of alternating K+ ions and water molecules in the selectivity filter demonstrates a starting configuration for a knock‐on conduction mechanism. Resting VSD/closed pore structure is shown using light‐blue contours, and activated VSD/open pore is shown using grey contours. α‐Helices are shown by white cylinders and loops by black/grey curves. Distorted (inactivated) selectivity filter (SF) is shown in pink. Charged residues on S4 are shown by blue/gray circles, K+ ions and water molecules in the SF are shown in purple and red, respectively. Illustrations are based on EAG (Whicher & MacKinnon, ) and hERG (Wang & MacKinnon, ) cryo‐EM structures.