Computer simulations are rapidly becoming a standard tool to study the structure and
dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased
simulations of lipid and membrane-active peptides. With the increasing number of high-
resolution structures of membrane proteins, which also enables homology modelling of
more structures, a wide range of membrane proteins can now be simulated over time spans
that capture essential biological processes. Longer time scales are accessible by special …

Developments in computational algorithms and structure-determination technologies have
enabled molecular dynamics simulations to become a routine tool to investigate the
structure and dynamics of biological membranes and membrane proteins in great detail. In
this chapter, we provide an overview of atomistic molecular dynamics simulations and
related methods, such as coarse-grain simulations and biased sampling methods, and
illustrate using key examples how such methods have advanced our understanding in the …