Study of the electrostatics treatment in molecular dynamics simulations

This article considers the treatment of long-range interactions in molecula r dynamics simulations. We investigate the effects of using different cutof f distances, constant versus distance-dependent dielectric, and different s moothing methods. In contrast to findings of earlier studies, we find that increasing the cutoff over 8 Angstrom does not significantly improve the ac curacy (Arnold and Ornstein, Proteins 1994;18:19-33), and using a distance- dependent dielectric instead of a constant dielectric also does not improve accuracy (Guenot and Kollman, Protein Sci 1992;1:1185-1205). This might de pend on differences in simulation protocols or force fields, or both, becau se we use the CHARMM22 force field with stochastic boundary conditions, whe reas earlier studies used other protocols and energy functions. We also not e that the stability of the simulations is highly dependent on the starting structure, showing that accurate molecular simulations not only depend on a realistic simulation protocol but also on correct initial conditions. Pro teins 1999;37: 417-428. (C) 1999 Wiley-Liss, Inc.