This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential depends explicitly on time to efficiently approximate the transient coarse-grained dynamics. We apply the path-space force matching approach at the transient dynamics regime to learn the proposed model parameters. In particular, we parameterize the coarse-grained potential both with respect to the pair distance of the CG particles and the time, and we obtain an evolution model that is explicitly time-dependent. Moreover, we follow a data-driven approach to estimate the friction kernel, given by appropriate correlation functions directly from the underlying all-atom molecular dynamics simulations. To explore and validate the proposed methodology we study a benchmark system of a moving particle in a box. We examine the suggested model's effectiveness in terms of the system's correlation time and find that the model can approximate well the transient time regime of the system, depending on the correlation time of the system. As a result, in the less correlated case, it can represent the dynamics for a longer time interval. We present an extensive study of our approach to a realistic high-dimensional water molecular system. Posing the water system initially out of thermal equilibrium we collect trajectories of all-atom data for the, empirically estimated, transient time regime. Then, we infer the suggested model and strengthen the model's validity by comparing it with simplified Markovian models.

翻译：本工作提出了一种系统方法，用于描述从全原子模拟数据推断出的粗粒化分子系统的瞬态动力学。我们建议采用朗之万型动力学，其中粗粒化相互作用势显式依赖于时间，以高效逼近瞬态粗粒化动力学。在瞬态动力学区域应用路径空间力匹配方法，学习所提模型参数。具体而言，我们同时针对粗粒化粒子的对距离和时间对粗粒化势进行参数化，从而得到显式时间依赖的演化模型。此外，我们采用数据驱动方法，通过底层全原子分子动力学模拟中的适当相关函数直接估计摩擦核。为探索和验证所提方法，我们以盒子中运动粒子为基准系统进行研究。考察该模型在系统关联时间方面的有效性，发现模型能够根据系统关联时间较好地逼近系统瞬态时间区间。结果表明，在关联性较弱的情况下，模型可在更长时间区间内表示动力学过程。我们针对实际高维水分子系统对该方法进行了广泛研究。将水系统初始置于热平衡之外，收集瞬态时间区间内（经验估计）全原子数据的轨迹。继而推断所提模型，并通过与简化马尔可夫模型对比，强化了模型的有效性。