Molecular Dynamics Simulation on the Connection Machine

Abstract

An algorithm for the efficient calculation of macromolecular force fields on the Connection Machine is described. The full force field is separated into bond interactions and non-bonding interactions. Only the latter are implemented on the Connection Machine, the former, less computationally intensive tasks are performed by an existing, conventional molecular dynamics code on the front end. Parallelization of the evaluation of non-bonding interactions is achieved by the Replicated Systolic Loop algorithm introduced in this paper. The algorithm is a variant of the Systolic Loop scheme often used for the computation of 2-particle forces for the classical N-particle problem.