Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.
Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant.
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DOI：
10.1021/ct200731v
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发表时间：
2012-01-10
影响因子：
5.5
通讯作者：
van der Spoel, David
中科院分区：
文献类型：
--
作者：
Caleman, Carl;van Maaren, Paul J.;Hong, Minyan;Hub, Jochen S.;Costa, Luciano T.;van der Spoel, David
有机小分子的化学组成通常与氨基酸侧链或核酸中的碱基非常相似，因此没有先验的理由解释为什么分子力学力场不能用单个参数集来描述有机液体和生物分子。在这里，我们设计了一个基准的力场，以测试现有的力场再现有机液体的一些关键特性，即密度，蒸发焓，表面张力，在恒定的体积和压力下的热容，等温压缩性，体积膨胀系数，静态介电常数的能力。超过1200个实验测量用于与146种有机液体的模拟进行比较。新的多项式插值的介电常数（32个分子），在恒定压力下的热容量（三个分子），和等温压缩性（53个分子）作为温度的函数，已经取得了实验数据的基础上，为了能够比较模拟结果。为了计算热容，我们应用两相热力学方法（Lin等人，J.Chem.Phys.2003，119，11792），其允许基于从速度自相关函数导出的状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新的实用程序中实现，名为g_dos，并给出了基本方程的详细描述。本工作的目的是建立两个流行的力场，OPLS/AA（液体模拟的全原子优化势）和GAFF（广义琥珀力场），以找到共同的瓶颈，即，特别是困难的分子，并作为未来力场发展的参考点。为了形成公平的竞争环境，所有分子都用相同的参数设置进行评估，例如恒温器和恒压器，静电相互作用的处理和系统大小（1000个分子）。基于使用Vanommeslaeghe等人提出的CHARMM通用力场（CGenFF）的模拟，来自独立数据集的蒸发密度和焓（J. Comput. 2010，31，671）用于比较。我们发现，总体而言，OPLS/AA力场的表现略好于GAFF，但有显着的问题与再现的表面张力和介电常数的两个力场。
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.
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影响因子：
4.4
作者：
Caleman, Carl;van der Spoel, David
通讯作者：
van der Spoel, David
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
6.3
作者：
BERENDSEN, HJC;VANDERSPOEL, D;VANDRUNEN, R
通讯作者：
VANDRUNEN, R
影响因子：
4.4
作者：
DITCHFIELD, R;HEHRE, WJ;POPLE, JA
通讯作者：
POPLE, JA
影响因子：
4.4
作者：
CURTISS, LA;MCGRATH, MP;RADOM, L
通讯作者：
RADOM, L