Efficient Molecular Dynamics (MD) simulation on Field Programmable Gate Array (FPGA)s with MultiGrid method

A Molecular Dynamic (MD) system is defined by the position and momentum of particles and their interactions. The dynamics of a system can be evaluated by an N-body problem and the simulation is continued until the energy reaches equilibrium. Thus, solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. The interactions of particles to be evaluated are short-ranged interactions and long-ranged interactions. We are focusing on the latter, since the calculation time is O(N) for an N particle system. There are many existing algorithms aimed at reducing the calculation time of MD simulations. Among the algorithms, Multigrid (MG) method [1] reduces O(N) calculation time to O(N) time while still achieving reasonable accuracy. Another movement to achieve much faster calculation time is running MD simulation on special purpose processors and customized hardware with ASICs or FPGAs.