Study of the electrostatics treatment in molecular dynamics simulations.
This article considers the treatment of long-range interactions in molecular dynamics simulations. We investigate the effects of using different cutoff distances, constant versus distance-dependent dielectric, and different smoothing methods. In contrast to findings of earlier studies, we find that increasing the cutoff over 8 A does not significantly improve the accuracy (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 depend on differences in simulation protocols or force fields, or both, because we use the CHARMM22 force field with stochastic boundary conditions, whereas earlier studies used other protocols and energy functions. We also note 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.
Garemyr
R
R
Department of Biochemistry, Stockholm University, Sweden.
Elofsson
A
A
D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013269:Stochastic Processes
D011506:Proteins