Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink’s group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.

中文翻译：

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重要生物学系统的粗粒度分子动力学理论与实践


与全原子分子动力学相比，粗粒度模型的分子动力学如今被广泛用于在大时间和尺寸尺度上模拟生物分子系统。在这篇综述文章中，我们描述了粗粒分子动力学的物理基础、粗粒力场、运动方程和各自的数值积分算法，并选择了粗粒分子动力学的实际应用。我们证明，粗粒位点的运动受平均力的势能以及摩擦力和随机力的控制，这些力是由二次自由度积分产生的。因此，朗之万动力学是在粗粒度水平上描述系统运动的自然方法，而平均力的势是粗粒度力场的物理基础。此外，粗粒度变量的选择以及粗粒度位置通常不具有球对称性的事实意味着非对角惯性张量。我们描述了分子动力学模拟中使用的选定的粗粒度模型，包括 Marrink 小组开发的最流行的 MARTINI 模型和我们实验室开发的生物大分子 UNICORN 模型。最后，我们讨论了应用粗粒度分子动力学研究生物学重要过程的例子。