Computer simulation of liquids
Computer simulation of liquids
Proceedings of the 1996 ACM fourth international symposium on Field-programmable gate arrays
The Art of Molecular Dynamics Simulation
The Art of Molecular Dynamics Simulation
Large Scale Simulation of Parallel Molecular Dynamics
IPPS '99/SPDP '99 Proceedings of the 13th International Symposium on Parallel Processing and the 10th Symposium on Parallel and Distributed Processing
A portable distributed implementation of the parallel multipole tree algorithm
HPDC '95 Proceedings of the 4th IEEE International Symposium on High Performance Distributed Computing
Reconfigurable Molecular Dynamics Simulator
FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Examining the Feasibility of Reconfigurable Models for Molecular Dynamics Simulation
ICA3PP '08 Proceedings of the 8th international conference on Algorithms and Architectures for Parallel Processing
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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.