Refining Coarse-Grained Molecular Topologies: A Bayesian Optimization Approach

TL;DR

This paper introduces a Bayesian Optimization method to refine Martini3 coarse-grained molecular topologies, enhancing accuracy for domain-specific applications while maintaining computational efficiency.

Contribution

It presents a novel Bayesian Optimization approach to optimize bonded interaction parameters in Martini3 CGMD, improving accuracy without sacrificing efficiency.

Findings

Optimized CG potential applicable to various polymer sizes

Achieved accuracy comparable to all-atom MD

Maintained computational speed of coarse-grained simulations

Abstract

Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated with All-Atom (AA) MD simulations have led to the development of Coarse-Grained Molecular Dynamics (CGMD), providing a lower-dimensional compression of the AA structure into representative CG beads, offering reduced computational expense at the cost of predictive accuracy. Existing CGMD methods, such as CG-Martini (calibrated against experimental data), aim to generate an embedding of a topology that sufficiently generalizes across a range of structures. Detrimentally, in attempting to specify parameterization with applicability across molecular classes, it is unable to specialize to domain-specific applications, where sufficient accuracy and computational speed are critical. This work presents a novel approach to optimize derived results from CGMD simulations by refining the general-purpose Martini3 topologies specifically the bonded interaction parameters within a given coarse-grained mapping - for domain-specific applications using Bayesian Optimization methodologies. We have developed and validated a CG potential applicable to any degree of polymerization, representing a significant advancement in the field. Our optimized CG potential, based on the Martini3 framework, aims to achieve accuracy comparable to AAMD while maintaining the computational efficiency of CGMD. This approach bridges the gap between efficiency and accuracy in multiscale molecular simulations, potentially enabling more rapid and cost-effective molecular discovery across various scientific and technological domains.