EdSr: A Novel End-to-End Approach for State-Space Sampling in Molecular Dynamics Simulation

TL;DR

EdSr introduces an adaptive timestep method for molecular dynamics, enabling larger timesteps and improved flexibility, potentially extending simulation time scales.

Contribution

It presents a novel end-to-end approach, EdSr, inspired by ODE and Taylor expansion, for dynamic timestep adjustment in MD simulations.

Findings

EdSr can operate with larger timesteps than velocity-Verlet.

It dynamically adjusts timestep based on simulation needs.

Demonstrated effectiveness across various models.

Abstract

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 equation and Taylor expansion formula, which enables flexible adjustment of timestep in MD simulations. By setting up four groups of experiments including simple functions, ideal physical models, all-atom simulations and coarse-grained simulations, we demonstrate that EdSr can dynamically and flexibly adjust the simulation timestep according to the requirements during simulation period, and operate with larger timesteps than the widely used velocity-Verlet integrator. Although the method can not perform perfectly at flexible timestep across all simulation systems, we believe that it provides a promising direction for future studies.