Ion channels are highly specific membrane-spanning proteinstructures which serve to facilitate the passage of selected ionsacross the lipid barrier. In the past decade, molecular dynamicssimulations based on atomic models and realistic microscopicinteractions with explicit solvent and membrane lipids have beenused to gain insight into the function of these complex systems.These calculations have considerably expanded our view of ionpermeation at the microscopic level. This Account will mainly focuson computational studies of the gramicidin A channel, one of thesimplest and best characterized molecular pore.