The past two decades have borne remarkable progress in the application of the molecular dynamics method in a number of engineering problems. However, the computational efficiency is limited by the massive-atoms system, and the study of rare dynamically-relevant events is challenging at the timescale of molecular dynamics. In this work, a multi-scale molecular simulation algorithm is proposed with a novel toy model that can mimic the state transitions in extensive scenarios. The algorithm consists of two scales, including producing the realistic particle trajectory and probability transition matrix in the molecular dynamics scale and calculating the state distribution and residence time in the Monte Carlo scale. A new state definition is proposed to take the velocity direction into consideration, and different coarsening models are established in the spatial and time scales. The accuracy, efficiency, and robustness of our proposed multi-scale method have been validated, and the general applicability is also demonstrated by explaining two practical applications in the shale gas adsorption and protein folding problems respectively.

过去二十年来，分子动力学方法在许多工程问题中的应用取得了显着进展。然而，计算效率受到大原子系统的限制，在分子动力学的时间尺度上研究罕见的动态相关事件具有挑战性。在这项工作中，提出了一种多尺度分子模拟算法，该算法具有一种新颖的玩具模型，可以模拟广泛场景中的状态转换。该算法由两个尺度组成，包括在分子动力学尺度上产生真实的粒子轨迹和概率转移矩阵，以及在蒙特卡罗尺度下计算状态分布和停留时间。提出了一个新的状态定义来考虑速度方向，并在空间和时间尺度上建立了不同的粗化模型。我们提出的多尺度方法的准确性、效率和鲁棒性已经得到验证，并且通过分别解释页岩气吸附和蛋白质折叠问题中的两个实际应用也证明了其普遍适用性。