EdSr: 分子動力学シミュレーションにおける状態空間サンプリングのための新しいエンドツーエンドアプローチ

The molecular dynamics (MD) simulation technique has been widely used in complex systems, but the accessible time scale is limited due to the requirement of small integration timesteps. Here, we propose a novel method, named exploratory dynamics sampling with recursion (EdSr), inspired by ordinary differential equations and the Taylor expansion formula, which enables flexible adjustment of time steps in MD simulations. By setting up five groups of experiments, including simple functions, ideal physical models, all-atom simulations, coarse-grained simulations, and dissipative particle dynamics simulations, we demonstrate that EdSr can dynamically and flexibly adjust the simulation time step according to the requirements during the simulation period and operate with larger time steps than the widely used velocity-Verlet integrator. Besides, we provide rEdSr to enhance the stability for simulation with a long time scale by mitigating the effect of velocity drift. Although the method cannot perform perfectly at flexible time steps across all simulation systems, we believe that it provides a promising direction for future studies.