计算机科学
分子动力学
统计物理学
多样性(控制论)
航程(航空)
化学空间
功能(生物学)
极限(数学)
采样(信号处理)
计算化学
化学
物理
数学
人工智能
工程类
航空航天工程
生物
数学分析
生物化学
滤波器(信号处理)
进化生物学
计算机视觉
药物发现
作者
Wilfred F. van Gunsteren,Chris Oostenbrink
标识
DOI:10.1021/acs.jcim.4c00823
摘要
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.
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