An Effective Compressed Sparse Preconditioner for Large Scale Biomolecular Simulations

Abstract

The natural preconditioner defined by local potentials is effective in the truncated Newton method for minimizing large scale biomolecular potential energy functions. This paper extends its definition, and proposes an algorithm for generating the sparse pattern of the preconditioner from the primary structure of a molecular system with N atoms. It shows that the implementation of the new compressed sparse preconditioner requires only a linear order of N memory locations. © Springer-Verlag 2004.