OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking.

ABSTRACT: While free energy surfaces are the crux of our understanding of many chemical and biological processes, their accuracy is generally unknown. Moreover, many developments to improve their accuracy are often complicated, limiting their general use. Luckily, several tools and guidelines are already in place to identify these shortcomings, but they are typically lacking in flexibility or fail to systematically determine how to improve the accuracy of the free energy calculation. To overcome these limitations, this work introduces OGRe, a Python package for optimal grid refinement in an arbitrary number of dimensions. OGRe is based on three metrics that gauge the confinement, consistency, and overlap of each simulation in a series of umbrella sampling (US) simulations, an enhanced sampling techn

SUBMITTER: Borgmans S 

PROVIDER: S-EPMC10753773 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature