Santos Lucianna Helene Silva, Pantano Sergio
Institut Pasteur de Montevideo, Montevideo, Uruguay.
Facultad de Química, Universidad de La República, Montevideo, Uruguay.
Biophys Rev. 2025 Mar 22;17(2):285-292. doi: 10.1007/s12551-025-01305-x. eCollection 2025 Apr.
Current developments in specialized software and computer power make the simulation of large molecular assemblies a technical possibility despite their computational cost. Coarse-grained (CG) approaches simplify molecular complexity and reduce computational costs while preserving intermolecular physical/chemical interactions. These methods enable virus simulations, making them more accessible to research groups with limited supercomputing resources. However, setting up and running molecular dynamics simulations of multimillion systems requires specialized molecular modeling, editing, and visualization skills. Moreover, many issues related to the computational setup, the choice of simulation engines, and the force fields that rule the intermolecular interactions require particular attention and are key to attaining a realistic description of viral systems at the fully atomistic or CG levels. Here, we provide an overview of the current challenges in simulating entire virus particles and the potential of the SIRAH force field to address these challenges through its implementations for CG and multiscale simulations.
尽管计算成本高昂，但专用软件和计算机能力的当前发展使得对大型分子组装体进行模拟在技术上成为可能。粗粒度（CG）方法简化了分子复杂性并降低了计算成本，同时保留了分子间的物理/化学相互作用。这些方法能够进行病毒模拟，使资源有限的研究团队更容易开展相关研究。然而，对包含数百万个系统的分子动力学模拟进行设置和运行需要专业的分子建模、编辑和可视化技能。此外，许多与计算设置、模拟引擎的选择以及支配分子间相互作用的力场相关的问题需要特别关注，并且是在全原子或CG水平上对病毒系统进行真实描述的关键。在此，我们概述了模拟整个病毒颗粒目前面临的挑战，以及SIRAH力场通过其CG和多尺度模拟实现来应对这些挑战的潜力。
