Minimizing the Lennard-Jones potential function on a massively parallel computer

  • Authors:
  • G. L. Xue;R. S. Maier;J. B. Rosen

  • Affiliations:
  • -;-;-

  • Venue:
  • ICS '92 Proceedings of the 6th international conference on Supercomputing
  • Year:
  • 1992

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Abstract

The Lennard-Jones potential energy function arises in the study of low-energy states of proteins and in the study of cluster statics. This paper presents a mathematical treatment of the potential function, deriving lower bounds as a function of the cluster size, in both two and three dimensional configurations. These results are applied to the minimization of a linear chain, or polymer, in two-dimensional space to illustrate the relationship between energy and cluster size. An algorithm is presented for finding the minimum-energy lattice structure in two dimensions. Computational results obtained on the CM-5, a massively parallel processor, support a mathematical proof showing an essentially linear relationship between minimum potential energy and the number of atoms in a cluster. Computational results for as many as 50000 atoms are presented. This largest case was solved on the CM-5 in approximately 40 minutes at an approximate rate of 1.1 32-bit gigaflops.