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| Format: | Preprint |
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2023
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| Online-Zugang: | https://arxiv.org/abs/2305.11886 |
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| _version_ | 1866917164322127872 |
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| author | Bosy, Michal Scroggs, Matthew W. Betcke, Timo Burman, Erik Cooper, Christopher D. |
| author_facet | Bosy, Michal Scroggs, Matthew W. Betcke, Timo Burman, Erik Cooper, Christopher D. |
| contents | The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to the accurate representation of the molecular surface and partial charges, and exact enforcement of the boundary conditions at infinity. However, the boundary element method is limited to linear equations and piecewise constant variations of the material properties. In this work, we present a scheme that couples finite and boundary elements for the Poisson--Boltzmann equation, where the finite element method is applied in a confined {\it solute} region, and the boundary element method in the external {\it solvent} region. As a proof-of-concept exercise, we use the simplest methods available: Johnson--Nédélec coupling with mass matrix and diagonal preconditioning, implemented using the Bempp-cl and FEniCSx libraries via their Python interfaces. We showcase our implementation by computing the polar component of the solvation free energy of a set of molecules using a constant and a Gaussian-varying permittivity. We validate our implementation against the finite difference code APBS (to 0.5\%), and show scaling from protein G B1 (955 atoms) up to immunoglobulin G (20\,148 atoms). For small problems, the coupled method was efficient, outperforming a purely boundary integral approach. For Gaussian-varying permittivities, which are beyond the applicability of boundary elements alone, we were able to run medium to large sized problems on a single workstation. Development of better preconditioning techniques and the use of distributed memory parallelism for larger systems remains an area for future work. We hope this work will serve as inspiration for future developments for molecular electrostatics with implicit solvent models. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2305_11886 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation Bosy, Michal Scroggs, Matthew W. Betcke, Timo Burman, Erik Cooper, Christopher D. Computational Physics 35 G.m; J.2 The Poisson--Boltzmann equation is widely used to model electrostatics in molecular systems. Available software packages solve it using finite difference, finite element, and boundary element methods, where the latter is attractive due to the accurate representation of the molecular surface and partial charges, and exact enforcement of the boundary conditions at infinity. However, the boundary element method is limited to linear equations and piecewise constant variations of the material properties. In this work, we present a scheme that couples finite and boundary elements for the Poisson--Boltzmann equation, where the finite element method is applied in a confined {\it solute} region, and the boundary element method in the external {\it solvent} region. As a proof-of-concept exercise, we use the simplest methods available: Johnson--Nédélec coupling with mass matrix and diagonal preconditioning, implemented using the Bempp-cl and FEniCSx libraries via their Python interfaces. We showcase our implementation by computing the polar component of the solvation free energy of a set of molecules using a constant and a Gaussian-varying permittivity. We validate our implementation against the finite difference code APBS (to 0.5\%), and show scaling from protein G B1 (955 atoms) up to immunoglobulin G (20\,148 atoms). For small problems, the coupled method was efficient, outperforming a purely boundary integral approach. For Gaussian-varying permittivities, which are beyond the applicability of boundary elements alone, we were able to run medium to large sized problems on a single workstation. Development of better preconditioning techniques and the use of distributed memory parallelism for larger systems remains an area for future work. We hope this work will serve as inspiration for future developments for molecular electrostatics with implicit solvent models. |
| title | Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation |
| topic | Computational Physics 35 G.m; J.2 |
| url | https://arxiv.org/abs/2305.11886 |