Suppr超能文献

用于凝聚相模拟并从中拟合非键合参数的工具包。

A Toolkit to Fit Nonbonded Parameters from and for Condensed Phase Simulations.

作者信息

Hédin Florent, El Hage Krystel, Meuwly Markus

机构信息

Department of Chemistry, University of Basel , Klingelbergstrasse 80, CH-4056 Basel, Switzerland.

Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States.

出版信息

J Chem Inf Model. 2016 Aug 22;56(8):1479-89. doi: 10.1021/acs.jcim.6b00280. Epub 2016 Aug 5.

Abstract

The quality of atomistic simulations depends decisively on the accuracy of the underlying energy function (force field). Of particular importance for condensed-phase properties are nonbonded interactions, including the electrostatic and Lennard-Jones terms. Permanent atomic multipoles (MTPs) are an extension to common point-charge (PC) representations in atomistic simulations. MTPs are commonly determined from and fitted to an ab initio Electrostatic Potential (ESP), and Lennard-Jones (LJ) parameters are obtained from comparison of experimental and computed observables using molecular dynamics (MD) simulations. For this a set of thermodynamic observables such as density, heat of vaporization, and hydration free energy is chosen, to which the parametrization is fitted. The current work introduces a comprehensive computing environment (Fitting Wizard (FW)) for optimizing nonbonded interactions for atomistic force fields of different qualities. The FW supports fitting of standard PC-based force fields and more physically motivated multipolar (MTP) force fields. A broader study including 20 molecules ranging from N-methyl-acetamide and benzene to halogenated benzenes, phenols, anilines, and pyridines yields a root mean squared deviation for hydration free energies of 0.36 kcal/mol over a range of 8 kcal/mol. It is furthermore shown that PC-based force fields are not necessarily inferior compared to MTP parametrizations depending on the molecule considered.

摘要

原子模拟的质量决定性地取决于基础能量函数(力场)的准确性。对于凝聚相性质而言,非键相互作用尤为重要,其中包括静电项和 Lennard-Jones 项。永久原子多极矩(MTPs)是原子模拟中对常见点电荷(PC)表示的一种扩展。MTPs 通常由从头算静电势(ESP)确定并拟合得到,而 Lennard-Jones(LJ)参数则通过使用分子动力学(MD)模拟比较实验和计算得到的可观测量来获得。为此,选择了一组热力学可观测量,如密度、汽化热和水合自由能,并对参数化进行拟合。当前工作引入了一个综合计算环境(拟合向导(FW)),用于优化不同质量的原子力场的非键相互作用。FW 支持对基于标准 PC 的力场和更具物理动机的多极(MTP)力场进行拟合。一项更广泛的研究涵盖了从 N-甲基乙酰胺、苯到卤代苯、苯酚、苯胺和吡啶等 20 种分子,在 8 kcal/mol 的范围内,水合自由能的均方根偏差为 0.36 kcal/mol。此外还表明,根据所考虑的分子,基于 PC 的力场不一定比 MTP 参数化差。

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验