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有机液体的力场基准:密度、汽化焓、热容、表面张力、等温压缩率、体积膨胀系数和介电常数。

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.

作者信息

Caleman Carl, van Maaren Paul J, Hong Minyan, Hub Jochen S, Costa Luciano T, van der Spoel David

出版信息

J Chem Theory Comput. 2012 Jan 10;8(1):61-74. doi: 10.1021/ct200731v. Epub 2011 Dec 7.

DOI:10.1021/ct200731v
PMID:22241968
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3254193/
Abstract

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.

摘要

小有机分子的化学成分通常与氨基酸侧链或核酸中的碱基非常相似,因此,从先验角度来看,没有理由认为分子力学力场不能用单一参数集来描述有机液体和生物分子。在此,我们设计了一个力场基准,以测试现有力场再现有机液体某些关键性质的能力,这些性质包括密度、汽化焓、表面张力、定容和定压热容、等温压缩率、体积膨胀系数以及静态介电常数。超过1200次实验测量数据被用于与146种有机液体的模拟结果进行比较。基于实验数据,对介电常数(32种分子)、定压热容(3种分子)和等温压缩率(53种分子)作为温度函数进行了新的多项式插值,以便能够将模拟结果与之比较。为了计算热容,我们应用了两相热力学方法(Lin等人,《化学物理杂志》2003年,119卷,11792页),该方法允许根据由速度自相关函数导出的态密度来计算热力学性质。该方法在GROMACS分子模拟软件包中的一个名为g_dos的新实用程序中实现,并给出了基础方程的详细阐述。这项工作的目的是确定两种流行力场OPLS/AA(用于液体模拟的全原子优化势)和GAFF(广义琥珀色力场)的当前水平,找出共同的瓶颈,即特别难处理的分子,并为未来力场的发展提供一个参考点。为了营造一个公平的竞争环境,所有分子都使用相同的参数设置进行评估,如恒温器和恒压器、静电相互作用的处理以及系统大小(1000个分子)。还纳入了基于Vanommeslaeghe等人(《计算化学杂志》2010年,31卷,671页)提出的CHARMM通用力场(CGenFF)模拟的独立数据集中的密度和汽化焓,以供比较。我们发现,总体而言,OPLS/AA力场的表现略优于GAFF,但这两种力场在再现表面张力和介电常数方面都存在重大问题。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c4d1/3254193/c85d0e2c8fe8/ct-2011-00731v_0008.jpg
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1
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2
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J Chem Theory Comput. 2006 Jan;2(1):1-11. doi: 10.1021/ct0502256.
3
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4
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