J.S. Conery, Dept. of Comput. & Inf. Sci., Oregon Univ., Eugene, OR, USA
W.L. Peticolas, Dept. of Comput. & Inf. Sci., Oregon Univ., Eugene, OR, USA
T. Rush, III, Dept. of Comput. & Inf. Sci., Oregon Univ., Eugene, OR, USA
K. Shanmugam, Dept. of Comput. & Inf. Sci., Oregon Univ., Eugene, OR, USA
J. Dominguez, Dept. of Comput. & Inf. Sci., Oregon Univ., Eugene, OR, USA
The Dreiding force field is a seven-term equation that describes the potential energy in a molecule as a function of the relative positions of bonded atoms and electrostatic interactions between atoms that do not share a bond. For large molecules such as DNA, with several thousand atoms, the O(n/sup 2/) nonbonded terms can require a significant amount of computation. We present a data-parallel algorithm that takes time O(n) on n processors. We compare the execution time of our algorithm on a MasPar MP-I with an efficient sequential program running on an SGI workstation.
Index Terms:
DNA; molecular biophysics; bioelectric phenomena; parallel algorithms; biology computing; parallel algorithm; potential energy; DNA; Dreiding force field; seven-term equation; molecule; bonded atoms; electrostatic interactions; nonbonded terms; data-parallel algorithm; execution time; MasPar MP-I; sequential program; SGI workstation; long polymeric structure; deoxyribonucleic acid
Citation:
J.S. Conery, W.L. Peticolas, T. Rush, III, K. Shanmugam, J. Dominguez, "A parallel algorithm for calculating the potential energy in DNA," hicss, pp.123, 28th Hawaii International Conference on System Sciences (HICSS'95), 1995
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