Molecular dynamics simulations of four different phases of a cationic surfactant dodecyltrimethylammonium chloride (DTAC) are presented. It is shown that when the topology of the initial configuration matches that of the equilibrium structure, the required equilibration times of MD simulations are only few nanoseconds. The methods of building initial configurations for simulations of the hexagonal and Ia3d bicontinuous cubic phases are described. The simulation results show that locally, the hydrophilic part of the hexagonal phase has a flat bilayer structure. Analysis of radial distribution functions shows that the properties of the hydrophilic layers of the phases are dominated by ion–ion and ion–water interactions. The dynamic properties of the system are dependent on the curvature of the aggregates, and calculated diffusion coefficients are in agreement with experimental NMR data.