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 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.<
>