A Boundary‐Integral Approach for the Poisson–Boltzmann Equation with Polarizable Force Fields. Issue 18 (19th March 2019)

• Record Type: Journal Article
• Authors: Cooper, Christopher D.
• Is Part Of: Journal of computational chemistry. Volume 40:Issue 18(2019)
• Page Start: 1680
• Page End: 1692
• Publication Date: 2019-03-19
• Subjects: Poisson–Boltzmann -- implicit solvent -- polarizable force fields -- boundary element method -- electrostatics; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.25820
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract : Implicit‐solvent models are widely used to study the electrostatics in dissolved biomolecules, which are parameterized using force fields. Standard force fields treat the charge distribution with point charges; however, other force fields have emerged which offer a more realistic description by considering polarizability. In this work, we present the implementation of the polarizable and multipolar force field atomic multipole optimized energetics for biomolecular applications (AMOEBA), in the boundary integral Poisson–Boltzmann solverPyGBe . Previous work from other researchers coupledAMOEBA with the finite‐difference solverAPBS, and found difficulties to effectively transfer the multipolar charge description to the mesh. A boundary integral formulation treats the charge distribution analytically, overlooking such limitations. This becomes particularly important in simulations that need high accuracy, for example, when the quantity of interest is the difference between solvation energies obtained from separate calculations, like happens for binding energy. We present verification and validation results of our software, compare it with the implementation onAPBS, and assess the efficiency ofAMOEBA and classical point‐charge force fields in a Poisson–Boltzmann solver. We found that a boundary integral approach performs similarly to a volumetric method onCPU . Also, we present aGPU implementation of our solver. Moreover, with a boundary element method, the mesh density to correctly resolve the electrostatic potential is the same for standard point‐charge and multipolar force fields. Finally, we saw that for binding energy calculations, a boundary integral approach presents more consistent results than a finite difference approximation for multipolar force fields. © 2019 Wiley Periodicals, Inc. Abstract : The electrostatics of biomolecular systems are modeled using a continuum approach, while describing the charge distribution inside the molecule with point multipoles that polarize. The authors parameterize the biomolecule with the atomic multipole optimized energetics for biomolecular applications force field and solve the electrostatic equations with a boundary integral formulation, which integrates the charge distribution analytically. The implementation is validated, which shows good behavior as the size of the biomolecule increases, and is tested for binding energy calculations.