Fast Surface Based Electrostatics for biomolecules modeling

TL;DR

This paper introduces a fast surface-based method (FSBE) for calculating biomolecular solvation energy, addressing inaccuracies in traditional Coulomb approximations and enabling efficient, stable energy computations for molecular dynamics simulations.

Contribution

The paper develops and validates a new surface-based approach (FSBE) that improves accuracy and efficiency in biomolecular electrostatics calculations compared to existing Coulomb approximation methods.

Findings

FSBE is only a few percent inaccurate across various molecular sizes.

Provides explicit reaction field potential and water polarization values.

Suitable for stable energy calculations in molecular dynamics simulations.

Abstract

We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of biomolecules with charged groups. The procedure is only a few percents wrong for molecular configurations of arbitrary sizes, provides explicit values for the reaction field potential at any point of the molecular interior, water polarization at the surface of the molecule, both the solvation energy value and its derivatives suitable for Molecular Dynamics (MD) simulations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as solvation energies contributions to a molecular complex formation.