RAPID CALCULATION OF ANY DIELECTRIC FUNCTION FOR MOLECULAR-DYNAMICS SIMULATIONS OF BIOLOGICAL MACROMOLECULES

Molecular dynamics simulations of macromolecules carrying charges, like nucleic acids, are hampered by proper treatment of the electrostatic problem. Although they can only constitute approximations, dielectric functions depending on the interatomic distance have the advantage of being easier to implement and faster to run than simulations with explicit solvent molecules and periodic boundary conditions. Further, their usefulness has been shown in several instances. Here, we describe a fast algorithm for calculating any dielectric function in MD simulations of biological macromolecules.