High‐Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi‐threading and distributed computing) used in all the natural sciences, including molecular biophysics. Next, we describe how these strategies are applied in molecular dynamics simulations and enhanced sampling methods, either based on force fields, on density functional theory or on QM/MM potentials. As test cases, we focus on the widely used CPMD and GROMACS packages, along with a hybrid QM/MM interface coupling the two recently developed by a European team including the Authors. The review closes with a short perspective on the use of HPC‐based biomolecular simulations.

中文翻译：

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生物分子模拟：高性能计算的视角

高性能计算正在影响包括分子生物物理学在内的所有生物医学科学。在这里，我们描述了包括分子生物物理学在内的所有自然科学中使用的通用并行计算策略（多线程和分布式计算）。接下来，我们将介绍如何基于力场，密度泛函理论或QM / MM势将这些策略应用于分子动力学模拟和增强的采样方法。作为测试用例，我们关注于广泛使用的CPMD和GROMACS软件包，以及将包括作者在内的欧洲团队最近开发的两者相结合的混合QM / MM接口。本文以基于HPC的生物分子模拟的简短视角作为结束语。