Abstract
A Molecular Dynamics (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. 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. 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 FPGAs. In this paper, we design and implement an FPGA-based MD simulator with an efficient MG method.
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Cho, E., Bourgeois, A.G., Tan, F. (2007). An FPGA Design to Achieve Fast and Accurate Results for Molecular Dynamics Simulations. In: Stojmenovic, I., Thulasiram, R.K., Yang, L.T., Jia, W., Guo, M., de Mello, R.F. (eds) Parallel and Distributed Processing and Applications. ISPA 2007. Lecture Notes in Computer Science, vol 4742. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74742-0_25
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DOI: https://doi.org/10.1007/978-3-540-74742-0_25
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