Assessment of linear finite-difference Poisson-Boltzmann solvers.
CPU time and memory usage are two vital issues that any numerical solvers for the Poisson-Boltzmann equation have to face in biomolecular applications. In this study, we systematically analyzed the CPU time and memory usage of five commonly used finite-difference solvers with a large and diversified set of biomolecular structures. Our comparative analysis shows that modified incomplete Cholesky conjugate gradient and geometric multigrid are the most efficient in the diversified test set. For the two efficient solvers, our test shows that their CPU times increase approximately linearly with the numbers of grids. Their CPU times also increase almost linearly with the negative logarithm of the convergence criterion at very similar rate. Our comparison further shows that geometric multigrid performs better in the large set of tested biomolecules. However, modified incomplete Cholesky conjugate gradient is superior to geometric multigrid in molecular dynamics simulations of tested molecules. We also investigated other significant components in numerical solutions of the Poisson-Boltzmann equation. It turns out that the time-limiting step is the free boundary condition setup for the linear systems for the selected proteins if the electrostatic focusing is not used. Thus, development of future numerical solvers for the Poisson-Boltzmann equation should balance all aspects of the numerical procedures in realistic biomolecular applications.
Wang
Jun
J
Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.
Luo
Ray
R
D000465:Algorithms; D019295:Computational Biology; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D016012:Poisson Distribution; D011506:Proteins / Q000737:chemistry*; D012996:Solutions; D055672:Static Electricity
D011506:Proteins; D012996:Solutions