Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program
The Journal of Supercomputing - Special issue on supercomputing in medicine
The Art of Molecular Dynamics Simulation
The Art of Molecular Dynamics Simulation
A portable distributed implementation of the parallel multipole tree algorithm
HPDC '95 Proceedings of the 4th IEEE International Symposium on High Performance Distributed Computing
Dynamic Reconfiguration: Architectures and Algorithms (Series in Computer Science (Kluwer Academic/Plenum Publishers).)
Reconfigurable Molecular Dynamics Simulator
FCCM '04 Proceedings of the 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines
Performance characterization of molecular dynamics techniques for biomolecular simulations
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
An FPGA design to achieve fast and accurate results for molecular dynamics simulations
ISPA'07 Proceedings of the 5th international conference on Parallel and Distributed Processing and Applications
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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. Many applications use MD for biomolecular simulations and the simulations are performed in multiscale of time and length. The simulations of the relevant scales require strong and fast computing power, but it is even beyond the reach of current fastest supercomputers. In this paper, we design R-Mesh Algorithms that require O(N) time complexity for the Direct method for MD simulations and O(r)+O(logM) time complexity for the Multigrid method, where r is N/M and M is the size of R-Mesh. Our work supports the theory that reconfigurable models are a good direction for biological studies which require high computing power.