Classical electrostatics for biomolecular simulations.
Classical electrostatics for biomolecular simulations.
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DOI：
10.1021/cr300461d
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发表时间：
2014-01-08
期刊：
影响因子：
62.1
通讯作者：
Sagui, Celeste
中科院分区：
文献类型：
--
作者：
Cisneros, G. Andres;Karttunen, Mikko;Ren, Pengyu;Sagui, Celeste
经典的原子模拟，也被称为分子力学模拟，使用简单的势能函数在原子水平上模拟分子系统。在这种表示中，原子或原子群被表示为球形粒子，它们通过胡克定律、伦纳德-琼斯和库仑势等相对简单的势函数相互作用。然后，通过蒙特卡罗、配体对接和分子动力学（MD）等模拟技术，将这些表征用于对分子的构象相空间进行采样。在MD模拟中，粒子服从经典的运动方程，通常是牛顿定律或朗之万动力学，这允许表征分子结构的时间演化，它们的波动和相互作用，从而研究系统的动力学和热力学性质。自20世纪50年代引入物理界以来，随着能量泛函的准确性和用于相关相空间采样的方法的复杂性的提高，1 MD方法变得越来越复杂。生物分子模拟中使用的力场包括一组基于物理模型的电位，以及一组通过拟合实验和/或量子模拟获得的相关参数。势仅仅是核坐标的数学函数，因为玻恩-奥本海默近似2允许电子自由度和核自由度的分离：经典力场明确考虑后者，而电子电荷由分布电荷或多极子近似。根据键距、键角和二面角，键合原子可以用二体、三体和四体来表示。非键相互作用通常由Lennard-Jones和Coulomb势来描述，通常用成对相互作用来描述。
Classical atomistic simulations, also known as molecular mechanics simulations, use simple potential-energy functions to model molecular systems at the atomic level. In this representation, atoms or groups of atoms are represented as spherical particles that interact through relatively simple potential functions such as Hooke’s law and Lennard-Jones and Coulomb potentials. These representations are then used to sample the conformational phase space of the molecules via simulation techniques such as Monte Carlo, ligand docking, and molecular dynamics (MD). In MD simulations, the particles obey classical equations of motion, generally Newton’s laws or Langevin dynamics, which allow for the characterization of the time evolution of the molecular structures, their fluctuations and interactions, and therefore the investigation of the system’s kinetic and thermodynamical properties. Since their introduction to the physics community during the 1950s, 1 MD methods have grown in complexity with refinements both of the accuracy of the energy functionals and of the sophistication of the methods used for the sampling of the relevant phase space. The force fields used in biomolecular simulations include a set of potentials based on physical models, along with a set of associated parameters which are obtained by fitting to experimental and/or quantum simulations. The potentials are mathematical functions of the nuclear coordinates only, since the Born− Oppenheimer approximation 2 allows the separation of the electronic and nuclear degrees of freedom: classical force fields consider explicitly the latter, while the electronic charge is approximated by distributed charges or multipoles. Bonded atoms are represented by two-body, three-body, and four-body terms, based on bond distances and bond and dihedral angles. Nonbonded interactions, commonly modeled by Lennard-Jones and Coulomb potentials, are generally described by pairwise interactions.
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影响因子：
3.3
作者：
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4.4
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