Data for: A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS

The integration of quantum mechanics and molecular mechanics (QM/MM) within molecular dynamics simulations is crucial to accurately model complex biochemical systems. Here, we present an enhanced implementation of the QM/MM interface in the GROMOS simulation package, introducing significant improvements in functionality and user control. We present new features, including the link atom scheme, which allows the modeling of QM regions as a part of bigger molecules. Benchmark tests on various systems, including QM water in water, amino acids in water, and tripeptides validate the reliability of the new functionalities. Performance evaluations demonstrate that the updated implementation is efficient, with the primary computational burden attributed to the QM program rather than the QM/MM interface or the MD program itself. The improved QM/MM interface enables more advanced investigations into biomolecular reactivity, enzyme catalysis, and other phenomena requiring detailed quantum mechanical treatment within classical simulations. This work represents a significant advancement in the capabilities of GROMOS, providing enhanced tools to explore complex molecular systems.

将量子力学（Quantum Mechanics, QM）与分子力学（Molecular Mechanics, MM）的整合方法（即QM/MM）应用于分子动力学模拟，对于精准建模复杂生化系统至关重要。本研究针对GROMOS模拟软件包中的QM/MM接口实现了增强版本，在功能与用户操控性上取得了显著提升。本次研究新增了多项功能，其中包括连接原子方案（link atom scheme），该方案支持将量子力学区域作为更大分子的一部分进行建模。针对多种体系开展的基准测试验证了新增功能的可靠性，测试体系涵盖水溶液中的QM水、水溶液中的氨基酸以及三肽。性能评估结果表明，更新后的实现方案具备高效性，其主要计算负载源于量子力学程序，而非QM/MM接口或分子动力学（Molecular Dynamics, MD）程序本身。经优化的QM/MM接口可支持对生物分子反应性、酶催化以及其他需在经典模拟中进行精细化量子力学处理的现象开展更深入的研究。本研究推动了GROMOS软件功能的重大升级，为复杂分子系统的探索提供了更为强大的工具。