# Accurate QM/MM Molecular Dynamics for Periodic Systems in \\textsc{GPU4PySCF} with Applications to Enzyme Catalysis

Source: [Accurate QM/MM Molecular Dynamics for Periodic Systems in \\textsc{GPU4PySCF} with Applications to Enzyme Catalysis](<https://www.sota2.com/research/paper/68fa48951e209131ce930a36>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-25T06:54:41.619Z

Authors: Chenghan Li, Garnet Kin-Lic Chan

Published: 2024-08-06T16:14:44.000Z

## Abstract

We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudo-bond treatment of the QM/MM boundary. We demonstrate that our method has well-controlled errors, stable self-consistent QM convergence, and energy-conserving dynamics. We further describe an application to the catalytic kinetics of chorismate mutase. Using an accurate hybrid functional reparametrized to coupled cluster energetics, our QM/MM simulations highlight the sensitivity in the calculated rate to the choice of quantum method, quantum region selection, and local protein conformation. Our work is provided through the open-source \\textsc{PySCF} package using acceleration from the \\textsc{GPU4PySCF} module.

## Recorded benchmark results

A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage.

## Original sources and implementation

[Original paper](<https://arxiv.org/abs/2408.03273>)

[PDF](<https://arxiv.org/pdf/2408.03273.pdf>)