GEM*：一种基于分子电子密度的分子动力学模拟力场。
GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations.
作者信息
Duke Robert E, Starovoytov Oleg N, Piquemal Jean-Philip, Cisneros G Andrés
机构信息
Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.
Sorbonne Universités , UPMC Univ Paris 06 , UMR 7616 Laboratoire de Chimie Théorique case courrier 137 , 4 place Jussieu 75005, Paris, France.
出版信息
J Chem Theory Comput. 2014 Apr 8;10(4):1361-5. doi: 10.1021/ct500050p. Epub 2014 Mar 3.
Abstract
GEM*, a force field that combines Coulomb and Exchange terms calculated with Hermite Gaussians with the polarization, bonded, and modified van der Waals terms from AMOEBA is presented. GEM* is tested on an initial water model fitted at the same level as AMOEBA. The integrals required for the evaluation of the intermolecular Coulomb interactions are efficiently evaluated by means of reciprocal space methods. The GEM* water model is tested by comparing energies and forces for a series of water oligomers and MD simulations. Timings for GEM* compared to AMOEBA are presented and discussed.
摘要
提出了GEM*，这是一种力场，它将用厄米特高斯函数计算的库仑项和交换项与来自AMOEBA的极化、键合和修正范德华项相结合。GEM在与AMOEBA相同水平拟合的初始水模型上进行了测试。分子间库仑相互作用评估所需的积分通过倒易空间方法有效地进行了评估。通过比较一系列水低聚物的能量和力以及分子动力学模拟对GEM水模型进行了测试。给出并讨论了GEM*与AMOEBA相比的计算时间。
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本文引用的文献
1
Distributed Multipole Analysis: Stability for Large Basis Sets.分布式多极分析：大基组的稳定性
J Chem Theory Comput. 2005 Nov;1(6):1128-32. doi: 10.1021/ct050190+.
2
Including Charge Penetration Effects in Molecular Modeling.在分子建模中纳入电荷穿透效应。
J Chem Theory Comput. 2010 Nov 9;6(11):3330-42. doi: 10.1021/ct1003862.
3
Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field.高斯静电模型（GEM）分布多极子在AMOEBA力场中的应用。
J Chem Theory Comput. 2012 Dec 11;8(12):5072-80. doi: 10.1021/ct300630u. Epub 2012 Sep 6.
4
Development of a "First Principles" Water Potential with Flexible Monomers: Dimer Potential Energy Surface, VRT Spectrum, and Second Virial Coefficient.具有柔性单体的“第一性原理”水势的发展：二聚体势能面、VRT光谱和第二维里系数。
J Chem Theory Comput. 2013 Dec 10;9(12):5395-403. doi: 10.1021/ct400863t. Epub 2013 Nov 25.
5
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.可极化分子动力学中极化能及相关作用力的可扩展评估：II. 迈向使用光滑粒子网格埃瓦尔德方法的大规模并行计算
J Chem Theory Comput. 2014 Feb 28;10(4):1638-1651. doi: 10.1021/ct401096t.
6
Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution.用于从电子分布的多极展开计算分子间相互作用能的静电贡献的改进公式。
J Phys Chem A. 2003 Dec 4;107(48):10353-9. doi: 10.1021/jp035748t.
7
Toward a Universal Water Model: First Principles Simulations from the Dimer to the Liquid Phase.迈向通用水模型：从二聚体到液相的第一性原理模拟
J Phys Chem Lett. 2012 Dec 20;3(24):3765-9. doi: 10.1021/jz3017733. Epub 2012 Dec 6.
8
Efficient optimization of van der Waals parameters from bulk properties.从体性质高效优化范德华参数。
J Comput Chem. 2013 Oct 15;34(27):2313-9. doi: 10.1002/jcc.23376. Epub 2013 Jul 5.
9
A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields.一种用于构建实用、高效的下一代基于轨道的量子力场的变分线性缩放框架。
J Chem Theory Comput. 2013 Mar 12;9(3):1417-1427. doi: 10.1021/ct3010134.
10
Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development.氢键的方向依赖性：基于密度的能量分解分析及其对力场发展的影响。
J Chem Theory Comput. 2011 Dec 13;7(12):4038-4049. doi: 10.1021/ct2003226.
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