DTU Chemistry, Technical University of Denmark (DTU), Kongens Lyngby, DK-2800, Denmark. Electronic address: https://twitter.com/@DavidCdeB.
Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, DE-52428, Germany.
Curr Opin Struct Biol. 2024 Jun;86:102821. doi: 10.1016/j.sbi.2024.102821. Epub 2024 Apr 29.
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes. However, leveraging the immense computational power of exascale computing requires innovative algorithms and software designs. In this context, we discuss the current status and future prospects of multiscale biomolecular simulations on exascale supercomputers with a focus on QM/MM MD. We highlight our own efforts in developing a versatile and high-performance multiscale simulation framework with the aim of efficient utilization of state-of-the-art supercomputers. We showcase its application in uncovering complex biological mechanisms and its potential for leveraging exascale computing.
生物系统和过程的复杂性跨越了从分子到宏观的多个尺度，因此需要使用多尺度模拟来全面理解。量子力学/分子力学（QM/MM）分子动力学（MD）模拟对于捕捉超出经典 MD 模拟范围的过程至关重要。而 exascale 计算的出现为科学探索提供了前所未有的机会，尤其是在生命科学领域，模拟是揭示生物过程中复杂分子机制的关键。然而，要充分利用 exascale 计算的巨大计算能力，需要创新的算法和软件设计。在此背景下，我们讨论了在 exascale 超级计算机上进行多尺度生物分子模拟的现状和未来前景，重点关注 QM/MM MD。我们强调了我们在开发多功能、高性能多尺度模拟框架方面的努力，旨在有效地利用最先进的超级计算机。我们展示了它在揭示复杂生物机制方面的应用及其在利用 exascale 计算方面的潜力。
