Free energy simulations.
Free energy simulations.
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DOI：
10.1111/j.1749-6632.1986.tb20933.x
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发表时间：
1986-01-01
影响因子：
5.2
通讯作者：
Beveridge, D L
中科院分区：
文献类型：
--
作者：
Mezei, M;Beveridge, D L
蒙特卡罗或分子动力学模拟涉及在高速数字计算机上对原子或分子组装的统计热力学和相关结构、能量学和（在MD的情况下）动力学特性的数值确定。分子系统的应用范围从研究分子或大分子中原子或原子团在分子内能量函数影响下的运动到基于分子间电位的凝聚态流体相（如液态水和水溶液）的结构和能量学的探索。在典型的蒙特卡罗或分子动力学模拟中确定的量包括平均或平均构型能量（热力学超额内能），平衡系统的各种空间分布函数和动力系统的时间相关函数，以及详细的结构和能量分析。溶液中分子的结构化学和反应化学中的各种问题，如溶剂化势、溶剂对构象稳定性的影响、溶剂对化学反应动力学和机理的影响等，也需要对构型自由能有一定的了解，原则上，构型自由能直接来自系统的统计热力学配分函数。分子模拟中对自由能的考虑对于分子内和分子间的自由度有明显不同的形式。对于分子内的情况，问题涉及分子内能量表面上的振动和振动运动模式。我们将在本文的最后简要讨论用于计算自由能的振动贡献的调和和准调和近似，但这里的重点仅限于分子间的情况，在这种情况下，系统的粒子进行扩散运动，调和或准调和处理被破坏。这些注意事项
Monte Carlo or molecular dynamics simulations involve the numerical determinations of the statistical thermodynamics and related structural, energetics and (in the case of MD) dynamical properties of an atomic or molecular assembly on a high speed digital computer. Applications to molecular systems range from the study of the motions of atoms or groups of atoms of a molecule or macromolecule under the influence of intramolecular energy functions to the exploration of the structure and energetics of condensed fluid phases such as liquid water and aqueous solutions based on intermolecular potentials. The quantities determined in a typical Monte Carlo or molecular dynamics simulation include the average or mean configurational energy (thermodynamic excess internal energy), various spatial distribution functions for equilibrium systems and time correlation functions for dynamical systems, along with detailed structural and energetic analyses thereof. Diverse problems in structural and reaction chemistry of molecules in solution, such as solvation potentials, solvent effects on conformational stability and the effect of solvent on chemical reaction kinetics and mechanism via activated complex theory also require a particular knowledge of the configurational free energy, which in principle follows directly from the statistical thermodynamic partition function for the system.Considerations on free energy in molecular simulations take a distinctly different form for intramolecular and intermolecular degrees of freedom. For the intramolecular case, the problem involves vibrational and librational modes of motion on the intramolecular energy surface. We will discuss briefly at the end of this paper the harmonic and quasiharmonic approximation used to compute vibrational contributions to the free energy but restrict the focus herein to the intermolecular case, where the particles of the system undergo diffusional motion and a harmonic or quasiharmonic treatment breaks down. These considerations