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Communication: Adaptive boundaries in multiscale simulations
The Journal of Chemical Physics ( IF 4.4 ) Pub Date : 2018-04-13 , DOI: 10.1063/1.5025826
Jason A. Wagoner 1 , Vijay S. Pande 2
Affiliation  

Combined-resolution simulations are an effective way to study molecular properties across a range of length and time scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of degrees of freedom required to accurately represent even a simple molecular process can vary by several orders of magnitude throughout the course of a simulation, and adaptive boundaries react to these changes to include an appropriate but not excessive amount of detail. Here, we derive the Hamiltonian and distribution function for such a molecular simulation. We also design an algorithm that can efficiently sample the boundary as a new coordinate of the system. We apply this framework to a mixed explicit/continuum simulation of a peptide in solvent. We use this example to discuss the conditions necessary for a successful implementation of adaptive boundaries that is both efficient and accurate in reproducing molecular properties.

中文翻译:

交流:多尺度模拟中的自适应边界

组合分辨率模拟是研究各种长度和时间范围内分子性质的有效方法。这些模拟可受益于自适应边界,该边界允许高分辨率区域随模拟的进行而适应(更改大小和/或形状)。在整个模拟过程中,准确表示一个简单的分子过程所需的自由度数可能会变化几个数量级,并且自适应边界会对这些变化做出反应,以包括适当但不过多的细节。在这里,我们推导了这种分子模拟的哈密顿函数和分布函数。我们还设计了一种算法,可以有效地将边界采样为系统的新坐标。我们将此框架应用于溶剂中肽段的混合显式/连续谱模拟。
更新日期:2018-04-14
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