Abstract
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.
•A multi-scale molecular simulation algorithm is developed in this paper in both molecular dynamics (MD) scale and Monte Carlo (MC) scale, and is proved to be accurate, robust and efficient.•A novel toy model is proposed for the first time to study typical state transition problems that can be applied in various engineering scenarios, which only needs one atom to generate the chaotic trajectory.•The sensitivities of the toy model are tested, including the effect of external force and channel size, in order to benefit further applications.•A new state definition is proposed to take the velocity direction into consideration, and different coarsening models are developed in the spatial and time scales.•The general applicability is demonstrated by explaining two practical applications in the shale gas adsorption and protein folding problems respectively.