CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.
CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.
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DOI：
10.1021/acs.jctc.1c00996
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发表时间：
2022-01-11
影响因子：
5.5
通讯作者：
Im W
中科院分区：
文献类型：
--
作者：
Choi YK;Kern NR;Kim S;Kanhaiya K;Afshar Y;Jeon SH;Jo S;Brooks BR;Lee J;Tadmor EB;Heinz H;Im W
分子建模和模拟是纳米科学的宝贵工具，可以预测纳米材料的机械，物理化学和热力学性质，并提供对潜在机制的分子水平洞察。然而，由于缺乏可靠和综合的网络基础设施，建立含有纳米材料的系统仍然具有挑战性。在这里，我们介绍了CHARMM-GUI中的Nanomaterial Modeler，这是一个基于网络的网络基础设施，提供了一个自动化的过程来生成各种纳米材料模型，相关的拓扑结构和配置文件，以使用大多数模拟软件包进行最先进的分子动力学模拟。纳米材料模型基于界面力场（IFF），这是最可靠的FF之一。通过单点能量计算评估了模拟程序之间纳米材料模型的可转移性，对于各种表面模型和平衡纳米颗粒形状，其产生了0.01%的相对绝对能量差。采用三种广泛使用的Lennard-Jones（LJ）截止值方法来评估纳米材料模型与传统生物分子FF的兼容性：r = 12 μ m（12截止值）的简单截断，10至12 μ m（10-12 fsw）的基于力的切换，以及无截止值的LJ颗粒网格Ewald（LJPME）。FF参数与这些LJ截止方法进行了广泛的验证，再现结构，界面和力学性能。我们发现，计算的密度和表面能与报道的实验结果是一致的，虽然模拟结果增加以下顺序：10-12 fsw < 12截止< LJPME;纳米材料中，LJ相互作用是一个主要组成部分显示相对较高的偏差（高达4%的密度和8%的表面能差异）相比，实验。Nanomaterial Modeler的能力也通过结合现有的CHARMM-GUI模块生成纳米材料-生物分子和纳米材料-聚合物界面的复杂系统来证明。我们希望Nanomaterial Modeler可以用于进行创新的纳米材料建模和模拟，以深入了解复杂纳米材料系统的结构，动力学和潜在机制。
Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here, we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topology, and configuration files to perform state-of-the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field (IFF), one of the most reliable FFs. The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely-used Lennard-Jones (LJ) cut-off methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cut-off), force-based switching over 10 to 12 Å (10–12 fsw), and LJ particle mesh Ewald with no cut-off (LJPME). The FF parameters with these LJ cut-off methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10–12 fsw < 12 cut-off < LJPME; nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared to the experiment. Nanomaterial Modeler’s capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulation to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems.
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影响因子：
1.5
作者：
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MacKerell, Alexander D., Jr.
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通讯作者：
MacKerell, Alexander D., Jr.
影响因子：
5.5
作者：
Choi YK;Park SJ;Park S;Kim S;Kern NR;Lee J;Im W
通讯作者：
Im W