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We have implemented classical Ewald and particle-mesh Ewald (PME) based treatments of fixed and induced point dipoles into the sander molecular dynamics (MD) module of AMBER 6. During MD the induced dipoles can be propagated along with the atomic positions either by iteration to self-consistency at each time step, or by a Car–Parrinello (CP) technique using an extended Lagrangian formalism. In this paper we present the derivation of the new algorithms and compare the various options with respect to accuracy, efficiency, and effect on calculated properties of a polarizable water model. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in large macromolecular systems.

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