Reweighted ensemble dynamics simulations: theory, improvement, and application

TL;DR

The paper introduces an improved reweighted ensemble dynamics (RED) method for more efficient sampling of complex biopolymer systems, enabling better exploration of metastable states and dynamical behaviors.

Contribution

It presents an enhancement to the RED method to reduce statistical errors and provides practical schemes for its application in complex molecular systems.

Findings

RED captures the topology of multiple-state transition networks

Detects diffusion-like dynamical behavior in entropy-dominated systems

Identifies solvent effects in solvated peptides

Abstract

Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable states. Here we further present an improvement to depress statistical errors of the RED and we discuss a few keys in practical application of the RED, provides schemes on selection of basis functions, determination of free parameter in the RED. We illustrate the application of the improvements in two toy models and in the solvated alanine dipeptide. The results show the RED enable to capture the topology of multiple-state transition networks, to detect the diffusion-like dynamical behavior in entropy-dominated system, and to identify solvent effects in the solvated peptides. The illustrations serve as general applications of the RED in more complex biopolymer systems.