Supporting Information for "Efficient and Reproducible RNA Molecular Dynamics Simulations in GROMACS: A Standardized Approach"

The Supporting Information includes all necessary files and data for reproducing the RNA molecular dynamics simulations conducted in this study. It contains system preparation files, including input structures, topology, and configuration scripts, along with GROMACS .mdp files for energy minimization, equilibration, and production runs. The force field parameters and solvation details are provided to ensure consistency in setup. Additionally, trajectory analysis scripts for RMSD, RMSF, radius of gyration, hydrogen bonding, and principal component analysis (PCA) are included. A comprehensive GROMACS command file is provided for seamless execution of the workflow. Processed results, including key plots and structural metrics, are also available.