Multigrid methods for classical molecular dynamics simulations of biomolecules

We present an O(N) multigrid-based method for the efficient calculation of the long-range electrostatic forces needed for biomolecular simulations, th at is suitable for implementation on massively parallel architectures. Alon g general lines, the method consists of: (i) a charge assignment scheme, wh ich both interpolates and smoothly assigns the charges onto a grid; (ii) th e solution of Poisson's equation on the grid via multigrid methods; and (ii i) the back interpolation of the forces and energy from the grid to the par ticle space. Careful approaches for the charge assignment and the force int erpolation, and a Hermitian approximation of Poisson's equation on the grid allow for the generation of the high-accuracy solutions required for high- quality molecular dynamics simulations. Parallel versions of the method sca le linearly with the number of particles for a fixed number of processors, and with the number of processors, for a fixed number of particles. (C) 200 1 American Institute of Physics.