A Poisson–Boltzmann dynamics method with nonperiodic boundary condition

We have developed a well-behaved and efficient finite difference Poisson–Boltzmann dynamics method with a nonperiodic boundary condition. This is made possible, in part, by a rather fine grid spacing used for the finite difference treatment of the reaction field interaction. The stability is also made possible by a new dielectric model that is smooth both over time and over space, an important issue in the application of implicit solvents. In addition, the electrostatic focusing technique facilitates the use of an accurate yet efficient nonperiodic boundary condition: boundary grid potentials computed by the sum of potentials from individual grid charges. Finally, the particle–particle particle–mesh technique is adopted in the computation of the Coulombic interaction to balance accuracy and efficiency in simulations of large biomolecules. Preliminary testing shows that the nonperiodic Poisson–Boltzmann dynamics method is numerically stable in trajectories at least 4 ns long. The new model is also fairly efficient: it is comparable to that of the pairwise generalized Born solvent model, making it a strong candidate for dynamics simulations of biomolecules in dilute aqueous solutions. Note that the current treatment of total electrostatic interactions is with no cutoff, which is important for simulations of biomolecules. Rigorous treatment of the Debye–Hückel screening is also possible within the Poisson–Boltzmann framework: its importance is demonstrated by a simulation of a highly charged protein.