FESTA: A Polygon-Based Approach for Extracting Relevant Structures from Free Energy Surfaces Obtained in Molecular Simulations

Journal of Chemical Information and Modeling, vol. 65, pp. 1–6

Abstract

An easy-to-use script named FESTA (Free Energy Surface Trajectory Analysis) is provided to streamline the extraction of equilibrium structures from free energy maps obtained with enhanced sampling simulation techniques and their associated trajectories. This approach efficiently identifies relevant structures by automatically selecting minima on the free energy surface using a connected-component labeling algorithm and extracts them utilizing a Shapely-polygon-based trajectory analysis process. The script is general and portable; it incorporates an automatic periodicity detection system; and multiprocessing is utilized to leverage all available computational resources for enhanced efficiency. The effectiveness of the proposed polygon-based approach is demonstrated through comparison with a naïve and largely inefficient loop-based script and its application across three distinct systems for benchmarking purposes.

Authors 2

1. Valentin Istomin Aachen Institute of Technical and Macromolecular Chemistry

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University , , Worringerweg 2 , ,

   Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany

2. GiovanniMaria Piccini corresponding

   University of Modena and Reggio Emilia

   Affiliation as printed

   University of Modena and Reggio Emilia , , Via G. Campi 103 , ,

   Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via G. Campi 103, 41125 Modena, Italy