On the Simulation of Complex Reactions Using Replica Exchange Molecular Dynamics (REMD)

Citation: XIN Liang, SUN Huai. On the Simulation of Complex Reactions Using Replica Exchange Molecular Dynamics (REMD)[J]. Acta Physico-Chimica Sinica, 2018, 34(10): 1179-1188. doi: 10.3866/PKU.WHXB201803161 shu

关于副本交换分子动力学模拟复杂化学反应的研究

辛亮 ^1,3, ,
孙淮 ^{1,2,3,
,}

1.
上海交通大学化学化工学院，上海 200240
2.
上海交通大学材料基因组联合研究中心，上海 200240
3.
吉林大学无机合成与制备化学国家重点实验室，长春 130012

通讯作者: 孙淮, huaisun@sjtu.edu.cn

基金项目:
国家自然科学基金 21173146

国家自然科学基金 21073119

国家自然科学基金(21073119, 21173146, 21473112)与国家重点基础研究发展规划项目(973) (2014CB239702)资助

国家重点基础研究发展规划项目(973) 2014CB239702

国家自然科学基金 21473112

摘要: 本文研究用温度副本交换分子动力学(T-REMD)和哈密顿副本交换分子动力学(H-REMD)方法模拟复杂化学反应的问题。使用具有不同活化能和反应能的简单置换反应模型，我们检验了上述两种方法用来预测反应平衡产物的效率和应用范围。T-REMD方法对具有适度活化能(约 < 20 kcal·mol^-1)或者反应能量(< 3 kcal·mol^-1)的放热反应是有效的。由于在相空间的不完整采样，对于同时具有高活化能和反应能量的反应其模拟效率有严重障碍，并且对于吸热反应问题更为显着。另一方面，H-REMD对一系列具有不同活化能的反应能的模型表现出色，与T-REMD相比，H-REMD可以使用更少的副本获得优异的结果。

关键词:

English

On the Simulation of Complex Reactions Using Replica Exchange Molecular Dynamics (REMD)

XIN Liang ^1,3, ,
SUN Huai ^{1,2,3,
,}

1.
School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
2.
Materials Genome Initiative Center, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
3.
State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Changchun 130012, P. R. China

Corresponding author: SUN Huai, huaisun@sjtu.edu.cn

Received Date: 08 February 2018
Accepted Date: 13 March 2018
Revised Date: 13 March 2018
Available Online: 15 October 2018
Fund Project:

The project was supported by the National Natural Science Foundation of China (21073119, 21173146, 21473112) and National Basic Research Program of China (973) (2014CB239702)

Abstract: A complex reaction, such as combustion, polymerization, and zeolite synthesis, involves a large number of elementary reactions and chemical species. Given a set of elementary reactions, the apparent reaction rates, population of chemical species, and energy distribution as functions of time can be derived using deterministic or stochastic kinetic models. However, for many complex reactions, the corresponding elementary reactions are unknown. Molecular dynamics (MD) simulation, which is based on forces calculated by using either quantum mechanical methods or pre-parameterized reactive force fields, offers a possibility to probe the reaction mechanism from the first principles. Unfortunately, most reactions take place on timescales far above that of molecular simulation, which is considered to be a well-known rare event problem. The molecules may undergo numerous collisions and follow many pathways to find a favorable route to react. Often, the simulation trajectory can be trapped in a local minimum separated from others by high free-energy barriers; thus, crossing these barriers requires prohibitively long simulation times. Due to this timescale limitation, simulations are often conducted on very small systems or at unrealistically high temperatures, which might hinder their validity. In order to model complex reactions under conditions comparable with those of the experiments, enhanced sampling techniques are required. The replica exchange molecular dynamics (REMD) is one of the most popular enhance sampling techniques. By running multiple replicas of a simulation system using one or several controlling variables and exchanging the replicas according to the Metropolis acceptance rule, the phase space can be explored more efficiently. However, most published work on the REMD method focuses on the conformational changes of biological molecules or simple reactions that can be described by a reaction coordinate. The optimized parameters of such simulations may not be suitable for simulations of complex reactions, in which the energy changes are much more dramatic than those associated with conformational changes and the hundreds elementary reactions through numerous pathways are unknown prior to the simulations. Therefore, it is necessary to investigate how to use the REMD method efficiently for the simulation of complex reactions. In this work, we examined the REMD method using temperature (T-REMD) and Hamiltonian (H-REMD) as the controlling variable respectively. In order to quantitatively validate the simulation results against direct simulations and analytic solutions, we performed the study based on a simple replacement reaction (A + BC = AB + C) with variable energy barrier heights and reaction energies described using the ReaxFF functional forms. The aim was to optimize the simulation parameters including number, sequence, and swap frequency of the replicas. The T-REMD method was found to be efficient for modeling exothermic reactions of modest reaction energy (< 3 kcal∙mol^-1) or activation energy (ca. < 20 kcal∙mol^-1). The efficiency was severely impaired for reactions with high activation and reaction energies. The analysis of the simulation trajectory revealed that the problem was intrinsic and could not be solved by adjusting the simulation parameters since the phase space sampled using T-REMD was localized in the region favored by high (artificial for speed-up) temperatures, which is different from the region favored by low (experimental) temperatures. This issue was aggravated in the case of endothermic reactions. On the other hand, the H-REMD run on a series of potential surfaces having different activation energies was demonstrated to be remarkably robust. Since the energy barrier only reduces the reaction rates, while the phase space controlled by the reaction energy differences remains unchanged at a fixed temperature, excellent results were obtained with fewer replicas by using H-REMD. It is evident that H-REMD is a more suitable method for the simulation of complex reactions.

Key words:

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

关于副本交换分子动力学模拟复杂化学反应的研究

通讯作者: 孙淮, huaisun@sjtu.edu.cn

English

On the Simulation of Complex Reactions Using Replica Exchange Molecular Dynamics (REMD)

Corresponding author: SUN Huai, huaisun@sjtu.edu.cn

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中国化学会秘书处

关于副本交换分子动力学模拟复杂化学反应的研究

通讯作者: 孙淮, huaisun@sjtu.edu.cn

English

On the Simulation of Complex Reactions Using Replica Exchange Molecular Dynamics (REMD)

Corresponding author: SUN Huai, huaisun@sjtu.edu.cn

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

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