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 nonbonded terms can require a significant amount of computation. In this paper we present a data-parallel algorithm that takes time on processors. We compare the execution time of our algorithm on a MasPar MP-1 with an efficient sequential program running on an SGI workstation.

• Type: Conference
• Year: 1995
• Where: HICSS
• Authors: John S. Conery, Warner L. Peticolas, Thomas Rush III, Kesavan Shanmugam, Jose Dominguez
• Keywords: Biometrics, Data-parallel Algorithm, Efficient Sequential Program, HICSS 1995, Seven-term Equation