Coordination schemes in distributed simulation of relativistic particle transport
Proceedings of the 2008 ACM symposium on Applied computing
Parallel and distributed particle collision simulation with decentralized control
GPC'08 Proceedings of the 3rd international conference on Advances in grid and pervasive computing
Hybrid dynamic iterations for the solution of initial value problems
Journal of Parallel and Distributed Computing
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Molecular Dynamics (MD) is an important atomistic simulation technique, with widespread use in computational chemistry, biology, and materials. An important limitation of MD is that the time step size is small, requiring a large number of iterations to simulate realistic time spans. Conventional parallelization is not very effective for this. We recently introduced a new approach to parallelization, where data from related prior simulations are used to parallelize a new computation along the time domain. In our prior work, the size of the physical system in the current simulation needed to be identical to that of the prior simulations. The significance of this paper lies in demonstrating a strategy that enables this approach to be used even when the physical systems differ in size. Furthermore, this method scaled up to almost processors with close to ideal speedup in one case, where conventional methods scale to only 2 - 3 processors.