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We review the state-of-the-art in computational molecular simulations for biological systems. We limit our discussion to three fields: all-atom simulations, coarse-grained models, and novel multiscale approaches. While molecular dynamics simulations are broadly used in the community, major efforts continue to be spent in pushing the boundaries in both size and time limits as well as in improvement of commonly-used force fields. Parallel to all-atom simulations, in recent times the development of coarse-grained methods has flourished. Such techniques are able to describe biophysical features of macromolecular complexes through the use of simplified model potentials. Finally, multiscale models are introduced, giving some perspective about possible future developments in this new field.