On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size
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DOI：
10.7554/elife.57589
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发表时间：
2020-08-19
期刊：
影响因子：
7.7
通讯作者：
de Groot, Bert L.
中科院分区：
文献类型：
--
作者：
Gapsys, Vytautas;de Groot, Bert L.
计算模拟，类似于湿实验室实验，受到统计波动的影响。评估这些波动的幅度，即对计算结果赋予不确定性，对于得出统计上可靠的结论至关重要。在这里，我们使用模拟箱大小作为自变量，以证明在得出有关潜在热力学和动力学效应的任何结论之前收集足够量的数据是多么重要。在不同的系统中，从溶剂化自由能到蛋白质的构象转变率，我们展示了如何建议的模拟箱大小的影响消失，增加采样。这表明，如果有的话，模拟箱的大小只最小限度地影响在这项工作中提出的生物分子系统的类型的热力学和动力学。
Computational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. Assessing the magnitude of these fluctuations, that is, assigning uncertainties to the computed results, is of critical importance to drawing statistically reliable conclusions. Here, we use a simulation box size as an independent variable, to demonstrate how crucial it is to gather sufficient amounts of data before drawing any conclusions about the potential thermodynamic and kinetic effects. In various systems, ranging from solvation free energies to protein conformational transition rates, we showcase how the proposed simulation box size effect disappears with increased sampling. This indicates that, if at all, the simulation box size only minimally affects both the thermodynamics and kinetics of the type of biomolecular systems presented in this work.