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Molecular conformation on the CM-5 by parallel two-level simulated annealing

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Abstract

In this paper, we propose a new kind of simulated annealing algorithm calledtwo-level simulated annealing for solving certain class of hard combinatorial optimization problems. This two-level simulated annealing algorithm is less likely to get stuck at a non-global minimizer than conventional simulated annealing algorithms. We also propose a parallel version of our two-level simulated annealing algorithm and discuss its efficiency. This new technique is then applied to the Molecular Conformation problem in 3 dimensional Euclidean space. Extensive computational results on Thinking Machines CM-5 are presented. With the full Lennard-Jones potential function, we were able to get satisfactory results for problems for cluster sizes as large as 100,000. A peak rate of over 0.8 giga flop per second in 64-bit operations was sustained on a partition with 512 processing elements. To the best of our knowledge, ground states of Lennard-Jones clusters of size as large as these have never been reported before.

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Authors and Affiliations

  1. Department of Computer Science and Electrical Engineering, University of Vermont, 05405, Burlington, VT

    Guoliang Xue

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  1. Guoliang Xue
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Also a researcher at the Army High Performance Computing Research Center, University of Minnesota, Minneapolis, MN 55415

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Xue, G. Molecular conformation on the CM-5 by parallel two-level simulated annealing. J Glob Optim 4, 187–208 (1994). https://doi.org/10.1007/BF01096722

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