Improved Sampling of Adaptive Path Collective Variables by Stabilized Extended-System Dynamics.

ABSTRACT: Because of the complicated multistep nature of many biocatalytic reactions, an a priori definition of reaction coordinates is difficult. Therefore, we apply enhanced sampling algorithms along with adaptive path collective variables (PCVs), which converge to the minimum free energy path (MFEP) during the simulation. We show how PCVs can be combined with the highly efficient well-tempered metadynamics extended-system adaptive biasing force (WTM-eABF) hybrid sampling algorithm, offering dramatically increased sampling efficiency due to its fast adaptation to path updates. For this purpose, we address discontinuities of PCVs that can arise due to path shortcutting or path updates with a novel stabilization algorithm for extended-system methods. In addition, we show how the convergence of simul

SUBMITTER: Hulm A 

PROVIDER: S-EPMC10753802 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature