Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers.
We implemented and optimized seven finite-difference solvers for the full nonlinear Poisson-Boltzmann equation in biomolecular applications, including four relaxation methods, one conjugate gradient method, and two inexact Newton methods. The performance of the seven solvers was extensively evaluated with a large number of nucleic acids and proteins. Worth noting is the inexact Newton method in our analysis. We investigated the role of linear solvers in its performance by incorporating the incomplete Cholesky conjugate gradient and the geometric multigrid into its inner linear loop. We tailored and optimized both linear solvers for faster convergence rate. In addition, we explored strategies to optimize the successive over-relaxation method to reduce its convergence failures without too much sacrifice in its convergence rate. Specifically we attempted to adaptively change the relaxation parameter and to utilize the damping strategy from the inexact Newton method to improve the successive over-relaxation method. Our analysis shows that the nonlinear methods accompanied with a functional-assisted strategy, such as the conjugate gradient method and the inexact Newton method, can guarantee convergence in the tested molecules. Especially the inexact Newton method exhibits impressive performance when it is combined with highly efficient linear solvers that are tailored for its special requirement.
Department of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
Qin
Q
Cai
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
Meng-Juei
MJ
Hsieh
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
Jun
J
Wang
Department of Biomedical Engineering, University of California, Irvine, CA 92697 ; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697.
Ray
R
Luo