Molecular dynamics simulations of biomolecules: Long-range electrostatic effects

Current computer simulations of biomolecules typically make use of classica l molecular dynamics methods, as a very large number (tens to hundreds of t housands) of atoms are involved over timescales of many nanoseconds. The me thodology for treating short-range bonded and van der Waals interactions ha s matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular syste ms, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation metho ds, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in sys tems with long-range interactions, and conclude with a short perspective on future trends.