Proceedings of the 28th Annual Hawaii International Conference on System Sciences- 1995 A Parallel Algorithm for Calculating the Potential Energy in DNA

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 0 (n2) nonbonded terms can require a signt$-cant amount of computation. In this paper we present a data-parallel algorithm that takes time 0 (n) on n pro-cessors. We compare the execution time of our algorithm on a MasPar MP-I with an efJicient sequential program running on an SGI workstation.