Kernel-based Minimal Distributed Charges: A Conformationally Dependent ESP-Model for Molecular Simulations

TL;DR

This paper introduces a kernel-based model that adaptively represents molecular electrostatic potential with off-center charges, significantly improving accuracy and enabling efficient, energy-conserving simulations of water molecules.

Contribution

The paper presents kMDCM, a novel conformationally dependent electrostatic model using Gaussian kernels, enhancing accuracy over traditional point charge models and enabling large-scale molecular dynamics.

Findings

ESP accuracy improved by at least a factor of two

Energy-conserving simulation of 2000 water molecules achieved

Model adapts to molecular geometry for better electrostatic representation

Abstract

A kernel-based method (kernelized minimal distributed charge model - kMDCM) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges whose positions adapts to the molecular geometry. Using Gaussian kernels and atom-atom distances as the features, the ESP for water and methanol is shown to improve by at least a factor of two compared with point charge models fit to an ensemble of structures. Combining kMDCM for the electrostatics and reproducing kernels for the bonded terms allows energy-conserving simulation of 2000 water molecules with periodic boundary conditions on the nanosecond time scale.