Acceleration of molecular mechanic simulation by parallelization and fast multipole techniques

摘要

Simulations of classical molecular dynamic (MD) systems can be sped up considerably by parallelizing the existing codes for distributed memory machines. In classical MD the CPU time is typically a function of the square of the number of atoms. The size of the molecular system which can be solved is therefore often limited by the CPU available. There are different approaches for reducing computation time. One consists in parallelizing sequential O(N~2) algorithms. The other is replacing the calculation of non-bonding forces by a less complex algorithm which can then be parallelized. We have generated a code (MEGADYN) for the simulation of MD of large simulation ensembles (up to l06 atoms) on the basis of classical force field methods. A reduction of complexity of the calculation of forces and energy down to O(N) was achieved by employing Greengards fast multipole method (FMM) to the Coulomb interaction. Within the framework of FMM the periodic boundary conditions are realized in a minimum image convention type manner. Thus MEGADYN can be used to simulate NVT as well as NPT ensembles.