Yulei Wang, Kaiqiang He, Dehua Dong, Jinxing Gu, Jefferson Zhe Liu, Yuxiang Wang
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引用次数: 0
摘要
六角环决定了许多纳米材料的机械强度、热稳定性和导电性,对其性能至关重要,因此这类结构在计算研究中受到了广泛关注。然而,现有的分子动力学(MD)模拟工具缺乏识别和表征这类结构的专门功能。为了填补这一空白,我们开发了六角环计算器(HexagonRingCalculator),这是一种直接从 MD 模拟数据中识别六角环并计算其几何特性(包括键长、环面积和圆度)的工具。该代码有助于分析温度变化等不同条件下的环变形。我们通过对石墨烯和纤维素进行经典和 ab initio MD 模拟,证明了它的功能性和准确性,突出了它在推进纳米材料计算研究方面的潜力。
HexagonRingCalculator: A Handy Code for Hexagonal Ring Characterization in Atomistic Simulations
Hexagonal rings are critical to the properties of many nanomaterials by determining their mechanical strength, thermal stability, and electrical conductivity, therefore this kind of structure has been intensively concerned in computational studies. However, existing molecular dynamics (MD) simulation tools lack specialized functions for identifying and characterizing them. To address this gap, we developed HexagonRingCalculator, a tool for identifying hexagonal rings and calculating their geometric properties, including bond lengths, ring area, and circularity, directly from MD simulation data. The code facilitates the analysis of ring deformation under varying conditions, such as temperature changes. We demonstrate its functionality and accuracy through classic and ab initio MD simulations of graphene and cellulose, highlighting its potential to advance computational studies in nanomaterials.
期刊介绍:
The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field.
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