System-specific parameter optimization for non-polarizable and polarizable force fields

TL;DR

This paper introduces a new implementation of the CTPOL model in OpenMM and an open-source tool for system-specific parameterization of force fields, improving accuracy in simulating cation-protein systems.

Contribution

The work presents a novel implementation of the CTPOL model and a parameterization tool, enabling more accurate force field customization for specific systems.

Findings

Successfully reproduces quantum chemistry energies

Demonstrates improved molecular dynamics simulations of a Zinc finger protein

Provides open-source tools for community use

Abstract

The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer and polarization effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding charge transfer (CT) and polarization (POL). Furthermore, we present an open-source parameterization tool, called FFAFFURR that enables the (system specific) parameterization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a Zinc finger protein.