Long Timescale Molecular Simulations for Understanding Ion Channel Function

This chapter introduces the basic methodology of molecular dynamics (MD) simulations, before discussing why it requires so much computational effort to conduct them and some of the algorithmic improvements utilized to ease the computational burden. MD simulations are a computationally intensive technique. The two main reasons for this include: force calculations and time step. The timescale of important biological events and the size of relevant biological systems dictate which questions can be addressed with MD simulations. The chapter explains the feasible duration of ion channel simulations. Examples of the use of some of the advanced sampling methods are given. To explain how MD simulations have been applied to understand the molecular basis of channel function, the chapter describes a number of studies that have used simulation to address an important question relating to channel function.