Efficient and accurate FPGA-based simulator for Molecular Dynamics
Eunjung Cho, Anu G. Bourgeois, José Alberto Fernández‐Zepeda · Proceedings - IEEE International Parallel and Distributed Processing Symposium · 2008
A Molecular Dynamics (MD) system is defined by the position and momentum of particles and their interactions. Solving the dynamics numerically and evaluating the interaction is computationally expensive even for a small number of particles in the system. We are focusing on long-ranged interactions, since the calculation time is O(N2) for an N particle system. There are many existing algorithms aimed at reducing the calculation time of MD simulations. Among the existing algorithms, Multigrid (MG) method [1] reduces O(N2) 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 an FPGAs. In this paper, we design and implement FPGA-based MD simulator with an efficient MG method.