刺突蛋白液滴模型的大规模FMO-MP2计算
Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model.
作者信息
Doi Hideo, Nakano Tatsuya, Sakakura Kota, Akisawa Kazuki, Okuwaki Koji, Hirano Yoshinori, Yamamoto Eiji, Yasuoka Kenji, Ohshima Satoshi, Katagiri Takahiro, Mochizuki Yuji
机构信息
Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Tokyo, Japan.
Department of HPC Support, Research Organization for Information Science and Technology, Kobe, Japan.
出版信息
J Comput Chem. 2025 Feb 5;46(4):e70052. doi: 10.1002/jcc.70052.
The spike protein of SARS-CoV-2 is a challenging target for theoretical approaches. Here we report a benchmark calculation of the spike protein droplet model by the fragment molecular orbital (FMO) at the second-order Møller-Plesset perturbation (MP2) level on the supercomputer Fugaku. One hundred structure samples from molecular dynamics (MD) simulations were used for both the closed and open forms of this protein (PDB IDs 6XLU and 6XM0 respectively). The number of total fragments is about 20,000, and the job time per structure was about 2 h on 8 racks of Fugaku.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的刺突蛋白是理论方法的一个具有挑战性的目标。在此，我们报告了在超级计算机富岳上，通过片段分子轨道（FMO）方法在二阶莫勒-普列斯特定理微扰（MP2）水平对刺突蛋白液滴模型进行的基准计算。来自分子动力学（MD）模拟的100个结构样本被用于该蛋白的封闭和开放形式（分别为PDB ID 6XLU和6XM0）。总片段数约为20,000个，在富岳的8个机架上，每个结构的计算时间约为2小时。
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