Chapter 4: Non-atomistic Simulations of Ion Channels

Mathematical modeling and numerical simulations are powerful tools for the analysis of the structure–function relation in ion channels. The continuous increase in the number of experimental structures of membrane proteins at high resolution has promoted the development of methods based on full atomistic descriptions of ion channels. However, the computational cost of atomistic simulations is still prohibitively high for a systematic study of conduction in ion channels. This chapter describes simplified models of conductions based on the implicit treatment of solvent molecules. In simplified models of ion channels, only a well-reasoned set of features is explicitly described. Thus, these methods are more than a mere way to increase the computational efficiency. Identifying which features are important, and how they impact on the functional properties, might offer a more profound understanding of the simulated systems. The chapter also discusses how to combine simplified models with atomistic simulations. These multi-scale models are a promising strategy to investigate the structure–function relation in complex biological molecules such as ion channels.