Recent developments in QM/MM methods towards open-boundary multi-scale simulations

被引：55

作者：

Pezeshki, Soroosh ^{[1
]}

Lin, Hai ^{[1
]}

机构：

[1] Univ Colorado, Dept Chem, Denver, CO 80217 USA

来源：

MOLECULAR SIMULATION | 2015年 / 41卷 / 1-3期

基金：

美国国家科学基金会;

关键词：

on-the-fly reclassification; adaptive partition; partial charge transfer; conservation of energy and momentum; electronegativity equalisation; POLARIZABLE FORCE-FIELD; DENSITY-FUNCTIONAL THEORY; MOLECULAR-DYNAMICS SIMULATIONS; ELECTRONEGATIVITY EQUALIZATION METHOD; MECHANICAL/MOLECULAR-MECHANICAL CALCULATIONS; FRACTIONAL PARTICLE NUMBER; EFFECTIVE GROUP POTENTIALS; FREE-ENERGY CALCULATIONS; DER-WAALS INTERACTIONS; HYBRID-ORBITAL METHOD;

D O I：

10.1080/08927022.2014.911870

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Combined quantum mechanics/molecular mechanics (QM/MM) methods have been widely used in multi-scale modelling and simulations of physical, chemical and biological processes in complex environments. In this review, we provide an overview of the recently developed QM/MM algorithms, with emphasis on our works, towards the ultimate goal of establishing an open boundary between the QM and MM subsystems. The open boundary is characterised by on-the-fly exchanges of partial charges and atoms between the QM and MM subsystems, allowing us to focus on the small QM subsystem of primary interest in dynamics simulations. An open-boundary scheme has the promise to the utilisations of small QM subsystems, high-levels of QM theory and long simulation times, which can potentially lead to new insights.

引用

页码：168 / 189

页数：22

共 31 条

[1] Affordable and accurate QM/MM multi-scale free energy simulations
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[9] Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK
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[10] QM/MM methods for large scale biochemical simulations: Implementation in NWChem computational chemistry package
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