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在具有谐振子力场的分子动力学模拟中实现反应活性。

Implementing reactivity in molecular dynamics simulations with harmonic force fields.

作者信息

Winetrout Jordan J, Kanhaiya Krishan, Kemppainen Joshua, In 't Veld Pieter J, Sachdeva Geeta, Pandey Ravindra, Damirchi Behzad, van Duin Adri, Odegard Gregory M, Heinz Hendrik

机构信息

Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, USA.

Materials Science and Engineering Program, University of Colorado at Boulder, Boulder, CO, USA.

出版信息

Nat Commun. 2024 Sep 11;15(1):7945. doi: 10.1038/s41467-024-50793-0.

Abstract

The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R). IFF-R is compatible with force fields for organic and inorganic compounds such as IFF, CHARMM, PCFF, OPLS-AA, and AMBER. Bond dissociation is enabled by three interpretable Morse parameters per bond type and zero energy upon disconnect. Use cases for bond breaking in molecules, failure of polymers, carbon nanostructures, proteins, composite materials, and metals are shown. The simulation of bond forming reactions is included via template-based methods. IFF-R maintains the accuracy of the corresponding non-reactive force fields and is about 30 times faster than prior reactive simulation methods.

摘要

从原子尺度到微米尺度对化学反应和力学性能(包括失效)进行模拟,在化学和材料科学领域仍然是一个长期存在的挑战。瓶颈包括计算可行性、可靠性和成本。我们引入了一种用于反应分子动力学模拟的方法,该方法通过用反应性的、能量守恒的莫尔斯势干净利落地替代非反应性经典谐振子键势,称为反应性界面力场(IFF-R)。IFF-R与有机和无机化合物的力场兼容,如IFF、CHARMM、PCFF、OPLS-AA和AMBER。每种键型通过三个可解释的莫尔斯参数实现键解离,断开时能量为零。展示了分子中键断裂、聚合物失效、碳纳米结构、蛋白质、复合材料和金属的用例。通过基于模板的方法包括了键形成反应的模拟。IFF-R保持了相应非反应性力场的准确性,并且比之前的反应性模拟方法快约30倍。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/963b/11391066/6537ee3195f6/41467_2024_50793_Fig1_HTML.jpg

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