A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
From MaRDI portal
Publication:4631997
Abstract: In this paper, a domain decomposition method for the Poisson-Boltzmann (PB) solvation model that is widely used in computational chemistry is proposed. This method, called ddLPB for short, solves the linear Poisson-Boltzmann (LPB) equation defined in using the van der Waals cavity as the solute cavity. The Schwarz domain decomposition method is used to formulate local problems by decomposing the cavity into overlapping balls and only solving a set of coupled sub-equations in balls. A series of numerical experiments is presented to test the robustness and the efficiency of this method including the comparisons with some existing methods. We observe exponential convergence of the solvation energy with respect to the number of degrees of freedom which allows this method to reach the required level of accuracy when coupling with quantum mechanical descriptions of the solute.
Recommendations
- A domain decomposition method for the polarizable continuum model based on the solvent excluded surface
- scientific article; zbMATH DE number 1269443
- A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
- A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
- Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
- A finite volume scheme for Nernst-Planck-Poisson systems with ion size and solvation effects
- Domain decomposition method for reaction-diffusion systems
- A domain decomposition method for advection-diffusion processes with application to blood solutes
- A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach
- scientific article; zbMATH DE number 961556
Cites work
- scientific article; zbMATH DE number 5669486 (Why is no real title available?)
- scientific article; zbMATH DE number 1313105 (Why is no real title available?)
- scientific article; zbMATH DE number 1953444 (Why is no real title available?)
- scientific article; zbMATH DE number 6159604 (Why is no real title available?)
- scientific article; zbMATH DE number 2208228 (Why is no real title available?)
- scientific article; zbMATH DE number 5038548 (Why is no real title available?)
- scientific article; zbMATH DE number 3273551 (Why is no real title available?)
- A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations
- A domain decomposition method for the polarizable continuum model based on the solvent excluded surface
- A hybrid solver of size modified Poisson-Boltzmann equation by domain decomposition, finite element, and finite difference
- A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule
- A quadrature formula for the sphere of the 131st algebraic order of accuracy
- A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics of solvated biomolecules
- AFMPB: an adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems
- Adaptive finite element modeling techniques for the Poisson-Boltzmann equation
- An efficient higher-order fast multipole boundary element solution for Poisson-Boltzmann-based molecular electrostatics
- Analysis of the parallel Schwarz method for growing chains of fixed-sized subdomains. I
- Analysis of the parallel Schwarz method for growing chains of fixed-sized subdomains. II
- Goal-oriented adaptivity and multilevel preconditioning for the Poisson-Boltzmann equation
- Mathematical analysis and calculation of molecular surfaces
- Mathematical methods for physicists. A comprehensive guide
- New applications of integral equations methods for solvation continuum models: Ionic solutions and liquid crystals
- New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
- Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy
- Quality meshing of implicit solvation models of biomolecular structures
- SDPBS web server for calculation of electrostatics of ionic solvated biomolecules
- The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation
- Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions
Cited in
(10)- Regularization methods for the Poisson-Boltzmann equation: comparison and accuracy recovery
- scientific article; zbMATH DE number 736333 (Why is no real title available?)
- Efficient calculation of fully resolved electrostatics around large biomolecules
- A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications
- A domain decomposition method for the polarizable continuum model based on the solvent excluded surface
- Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation
- A Cartesian FMM-accelerated Galerkin boundary integral Poisson-Boltzmann solver
- Solution decomposition for the nonlinear Poisson-Boltzmann equation using the range-separated tensor format
- scientific article; zbMATH DE number 1269443 (Why is no real title available?)
- A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach
This page was built for publication: A Domain Decomposition Method for the Poisson--Boltzmann Solvation Models
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q4631997)
