#Figures

All spectra (NMR, infrared, UV/Visible), molecular models, and plots presented in the main text and Supplementary Information are available in this directory. 

# Classical Molecular Dynamic (MD) and Metadynamics Simulations (metaD) Data and Analysis

This part of the repository contains data, parameters and scripts used in classical MD (oxi_MD, cov_MD and red_MD models) and meta-dynamics simulations (oxi_metaD, cov_metaD and red_metaD models) presented in our publication, including files essential for running metaD simulations, collective variable (COLVAR) analysis, and data processing for publication figures. Each directory contains a README file with instructions on file usage, script dependencies, and suggested analysis methods.

## Contents

#### MD and metaD Simulation Files

- Input Files: MD and metaD input files used to initialize and configure the simulations, including system setup, force field parameters, and environment settings.

- MetaD Parameters: Parameter files used for metaD simulations, detailing the biasing parameters, collective variables, and simulation controls.

#### HILLS and COLVAR Files

- HILLS Files: Files containing the metaD hills added during simulations, providing information on biasing potentials over time.

- COLVAR Files: Files capturing the values of the collective variables (CVs) during the simulations, enabling analysis of CV-based system evolution

#### Post-Processing Scripts

- Data Analysis and Plotting Scripts: these scripts used to analyze metaD data, including COLVAR data parsing and bias potential extraction and plotting investigated variables over simulation time.

- Extracting Max Bias during metaD Simulations: Provides the script used for extracting the maximum bias values from COLVAR files in metaD models.