Software Infrastructure for Next-Generation QM/MM−ΔMLP Force Fields

• Published in: The journal of physical chemistry. B 2024-07, Vol.128 (26), p.6257-6271
• Main Authors: Giese, Timothy J., Zeng, Jinzhe, Lerew, Lauren, McCarthy, Erika, Tao, Yujun, Ekesan, Şölen, York, Darrin M.
• Format: Article
• Language: English
• Subjects: B: Biophysical and Biochemical Systems and Processes
• ISSN: 1520-6106; 1520-5207; 1520-5207
• DOI: 10.1021/acs.jpcb.4c01466

We present software infrastructure for the design and testing of new quantum mechanical/molecular mechanical and machine-learning potential (QM/MM−ΔMLP) force fields for a wide range of applications. The software integrates Amber’s molecular dynamics simulation capabilities with fast, approximate quantum models in the xtb package and machine-learning potential corrections in DeePMD-kit. The xtb package implements the recently developed density-functional tight-binding QM models with multipolar electrostatics and density-dependent dispersion (GFN2-xTB), and the interface with Amber enables their use in periodic boundary QM/MM simulations with linear-scaling QM/MM particle-mesh Ewald electrostatics. The accuracy of the semiempirical models is enhanced by including machine-learning correction potentials (ΔMLPs) enabled through an interface with the DeePMD-kit software. The goal of this paper is to present and validate the implementation of this software infrastructure in molecular dynamics and free energy simulations. The utility of the new infrastructure is demonstrated in proof-of-concept example applications. The software elements presented here are open source and freely available. Their interface provides a powerful enabling technology for the design of new QM/MM−ΔMLP models for studying a wide range of problems, including biomolecular reactivity and protein–ligand binding.