Nucleic acids are highly charged polyelectrolytes. Their interactions with counterions are of great importance for their structural stability, conformational behaviour and biological functions. Molecular modelling and simulation techniques, particularly molecular dynamics, have been highly useful for studies of interactions between DNA, water and ions at the molecular level, allowing us to explain many experimental observations, or to obtain information not accessible experimentally. In this review we focus on both atomistic and coarse-grained molecular simulation studies concerning the interactions of DNA with different types of counterions, with emphasis on recent studies, still open questions, limits of the method and possible further developments.