Computer simulation of liquids
Computer simulation of liquids
Computer simulation using particles
Computer simulation using particles
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
NAMD2: greater scalability for parallel molecular dynamics
Journal of Computational Physics - Special issue on computational molecular biophysics
Concurrency and Computation: Practice & Experience - 2002 ACM Java Grande–ISCOPE Conference Part II
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Dynamic development of parallel computers makes them standard tool for large simulations. The technology achievements are not followed by the progress in scalable code design. The molecular dynamics is a good example. In this paper we present novel approach to the molecular dynamics which is based on the new asynchronous parallel algorithm inspired by the novel computer architectures. We present also implementation of the algorithm written in Java. Presented code is object-oriented, multithread and distributed. The performance data is also available.