FESTA: A Polygon-Based\nApproach for Extracting Relevant\nStructures from Free Energy Surfaces Obtained in Molecular Simulations

An\neasy-to-use script named FESTA (Free Energy Surface Trajectory\nAnalysis) is provided to streamline the extraction of equilibrium\nstructures from free energy maps obtained with enhanced sampling simulation\ntechniques and their associated trajectories. This approach efficiently\nidentifies relevant structures by automatically selecting minima on\nthe free energy surface using a connected-component labeling algorithm\nand extracts them utilizing a Shapely-polygon-based trajectory analysis\nprocess. The script is general and portable; it incorporates an automatic\nperiodicity detection system; and multiprocessing is utilized to leverage\nall available computational resources for enhanced efficiency. The\neffectiveness of the proposed polygon-based approach is demonstrated\nthrough comparison with a naïve and largely inefficient loop-based\nscript and its application across three distinct systems for benchmarking\npurposes.