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本文引用的文献

1
Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton.从从头算分子动力学模拟定义凝聚相反应力场:水合过量质子的案例。
J Chem Theory Comput. 2010 Oct 12;6(10):3223-32. doi: 10.1021/ct1004438. Epub 2010 Sep 23.
2
Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations.用于哈特里-福克交换计算的辅助密度矩阵方法。
J Chem Theory Comput. 2010 Aug 10;6(8):2348-64. doi: 10.1021/ct1002225. Epub 2010 Jul 1.
3
Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining.用于多尺度粗粒化的高效、正则化且可扩展的算法
J Chem Theory Comput. 2010 Mar 9;6(3):954-65. doi: 10.1021/ct900643r. Epub 2010 Jan 27.
4
Efficient Approach to Reactive Molecular Dynamics with Accurate Forces.基于精确力场的反应分子动力学高效方法。
J Chem Theory Comput. 2009 Nov 10;5(11):2925-9. doi: 10.1021/ct900301d.
5
On Ion and Molecular Polarization of Halides in Water.论卤化物在水中的离子与分子极化
J Chem Theory Comput. 2009 Jun 9;5(6):1449-53. doi: 10.1021/ct900096n.
6
CRYSCOR: a program for the post-Hartree-Fock treatment of periodic systems.CRYSCOR:用于处理周期性体系的 Hartree-Fock 后处理的程序。
Phys Chem Chem Phys. 2012 Jun 7;14(21):7615-28. doi: 10.1039/c2cp23927b. Epub 2012 Feb 15.
7
Re-examining the properties of the aqueous vapor-liquid interface using dispersion corrected density functional theory.利用色散修正密度泛函理论重新考察水汽液界面的性质。
J Chem Phys. 2011 Sep 28;135(12):124712. doi: 10.1063/1.3633239.
8
The curious case of the hydrated proton.水合质子的奇案。
Acc Chem Res. 2012 Jan 17;45(1):101-9. doi: 10.1021/ar200140h. Epub 2011 Aug 22.
9
Real-world predictions from ab initio molecular dynamics simulations.基于第一性原理分子动力学模拟的实际应用预测。
Top Curr Chem. 2012;307:109-53. doi: 10.1007/128_2011_195.
10
Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.经验价键反应势能面模型:并行多层次遗传程序方法。
J Chem Phys. 2011 Jul 28;135(4):044115. doi: 10.1063/1.3610907.

多尺度反应分子动力学。

Multiscale reactive molecular dynamics.

机构信息

Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, Illinois 60439, USA.

出版信息

J Chem Phys. 2012 Dec 14;137(22):22A525. doi: 10.1063/1.4743958.

DOI:10.1063/1.4743958
PMID:23249062
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3432097/
Abstract

Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

摘要

许多对化学、材料科学和生物学很重要的过程,如果不考虑电子和核级别的动力学及其与系统较慢、协作运动的耦合,就无法描述。这些固有的多尺度问题需要计算效率高且准确的方法来收敛统计性质。本文提出了一种方法,该方法使用来自凝聚相从头算模拟的直接数据来开发反应性分子动力学模型,而不需要预定义的经验函数。相反,反应性模型中使用的相互作用表示为通过使用线性最小二乘算法进行优化的插值函数的线性组合。这里概述的过程的一个显著优点是能够最小化需要非线性优化的参数数量。该方法可一般应用于多尺度问题,并通过直接基于凝聚相从头算分子动力学模拟为水合过剩质子和氢氧根离子生成反应性模型来证明。由此产生的模型忠实地再现了从头算模拟中的水-离子结构特性和扩散常数。此外,质子转移的自由能曲线也被再现,质子转移对两个离子在水中的结构扩散很敏感。这些模型与从头算模拟的高度一致性将允许以比当前从头算模拟方法高几个数量级的计算效率对凝聚相系统中的一般化学反应进行精确建模,从而有效地对系统较慢、大规模运动的耦合进行统计抽样。