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化学中的经典力学分子模拟方法:成就、局限、展望。

Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives.

机构信息

Institute for Molecular Physical Science, Swiss Federal Institute of Technology, ETH, CH-8093 Zurich, Switzerland.

Institute of Molecular Modelling and Simulation, BOKU University, 1190 Vienna, Austria.

出版信息

J Chem Inf Model. 2024 Aug 26;64(16):6281-6304. doi: 10.1021/acs.jcim.4c00823. Epub 2024 Aug 13.

Abstract

More than a half century ago it became feasible to simulate, using classical-mechanical equations of motion, the dynamics of molecular systems on a computer. Since then classical-physical molecular simulation has become an integral part of chemical research. It is widely applied in a variety of branches of chemistry and has significantly contributed to the development of chemical knowledge. It offers understanding and interpretation of experimental results, semiquantitative predictions for measurable and nonmeasurable properties of substances, and allows the calculation of properties of molecular systems under conditions that are experimentally inaccessible. Yet, molecular simulation is built on a number of assumptions, approximations, and simplifications which limit its range of applicability and its accuracy. These concern the potential-energy function used, adequate sampling of the vast statistical-mechanical configurational space of a molecular system and the methods used to compute particular properties of chemical systems from statistical-mechanical ensembles. During the past half century various methodological ideas to improve the efficiency and accuracy of classical-physical molecular simulation have been proposed, investigated, evaluated, implemented in general simulation software or were abandoned. The latter because of fundamental flaws or, while being physically sound, computational inefficiency. Some of these methodological ideas are briefly reviewed and the most effective methods are highlighted. Limitations of classical-physical simulation are discussed and perspectives are sketched.

摘要

半个多世纪以前,人们开始使用经典力学运动方程在计算机上模拟分子系统的动力学,从此,经典物理分子模拟成为化学研究的一个不可或缺的部分。它被广泛应用于化学的各个分支,为化学知识的发展做出了重大贡献。它提供了对实验结果的理解和解释,对可测量和不可测量物质性质的半定量预测,并允许在实验无法达到的条件下计算分子系统的性质。然而,分子模拟建立在许多假设、近似和简化的基础上,这些假设、近似和简化限制了它的适用范围和准确性。这些问题涉及到所使用的势能函数、分子系统的巨大统计力学构象空间的充分采样,以及从统计力学系综中计算化学系统特定性质的方法。在过去的半个世纪中,人们提出了各种改进经典物理分子模拟效率和准确性的方法思路,对这些方法思路进行了研究、评估、在通用模拟软件中实现或被放弃。后一种情况是因为存在根本缺陷,或者虽然在物理上合理,但计算效率低下。本文简要回顾了其中一些方法思路,并突出了最有效的方法。讨论了经典物理模拟的局限性,并勾勒了未来的发展方向。

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