Enveloped viruses, such as SARS-CoV-2, infect cells via fusion of their envelope with the host membrane. By employing molecular simulations to characterize viral envelopes, researchers can gain insights into key determinants of infection. Here, the Frontera supercomputer is leveraged for large-scale modeling and analysis of authentic viral envelopes, whose lipid compositions are complex and realistic. Visual Molecular Dynamics (VMD) with support for MPI is employed, overcoming previous computational limitations and enabling investigation into virus biology at an unprecedented scale. The techniques applied here to an authentic HIV-1 envelope at two levels of spatial resolution (29 million particles and 280 million atoms) are broadly applicable to the study of other viruses. The authors are actively employing these techniques to develop and characterize an authentic SARS-CoV-2 envelope. A general framework for carrying out scalable analysis of simulation trajectories on Frontera is presented, expanding the utility of the machine in humanity's ongoing fight against infectious diseases.

中文翻译：

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FRONTERA 上真实病毒包膜的可扩展分析


有包膜病毒，例如 SARS-CoV-2，通过包膜与宿主膜融合来感染细胞。通过利用分子模拟来表征病毒包膜，研究人员可以深入了解感染的关键决定因素。在这里，Frontera 超级计算机用于对真实病毒包膜进行大规模建模和分析，其脂质成分复杂而真实。采用支持 MPI 的视觉分子动力学 (VMD)，克服了之前的计算限制，并能够以前所未有的规模对病毒生物学进行研究。这里应用于两个空间分辨率水平（2900 万个粒子和 2.8 亿个原子）的真实 HIV-1 包膜的技术广泛适用于其他病毒的研究。作者正在积极利用这些技术来开发和表征真实的 SARS-CoV-2 包膜。提出了在 Frontera 上对模拟轨迹进行可扩展分析的通用框架，扩展了该机器在人类与传染病的持续斗争中的效用。