Collective mode mining from molecular dynamics simulations: a comparative approach
Collective mode mining from molecular dynamics simulations: a comparative approach
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DOI：
10.1142/s0219876218501086
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发表时间：
2017-09
期刊：
影响因子：
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通讯作者：
V. D. Camiola;V. Tozzini
中科院分区：
文献类型：
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作者：
V. D. Camiola;V. Tozzini
集体模的计算是分子动力学模拟分析的基础。有几种方法可用于提取这些信息，即轨道的简正模分析、主成分和谱分析，基本上不同的是被认为是节点的量（频率、振幅或位移模式），并导致不同种类的集体激励和物理谱可观测量的定义。不同的观点在谐波制度和/或同质原子系统中会聚。然而，对于非谐和非平衡动力学，不同的量带来不同的信息，只有它们的比较才能给出系统行为的完整视图。为了允许这样的比较分析，我们回顾和比较不同的方法，将它们以不同的组合应用于两个物理相关的例子：石墨烯和富勒烯C60。
The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e normal mode analysis, principal component and spectral analysis of trajectories, basically differing by the quantity considered as the nodal one (frequency, amplitude, or pattern of displacement) and leading to the definition of different kinds of collective excitations and physical spectral observables. Different views converge in the harmonic regime and/or for homo-atomic systems. However, for anharmonic and out of equilibrium dynamics different quantities bring different information and only their comparison can give a complete view of the system behavior. To allow such a comparative analysis, we review and compare the different approaches, applying them in different combination to two examples of physical relevance: graphene and fullerene C60.