This release provides scripts and associated molecular dynamics (MD) data for constructing and analyzing Markov state models (MSMs) from MD trajectories. The repository includes: Python scripts for MD trajectory analysis and MSM construction Input features and analysis pipelines for tICA and MSM analysis MD datasets generated under reduced and oxidized 2Fe–2S conditions Example workflows and input files related to AlphaFold3-based structure generation The analysis pipeline consists of: Feature extraction from MD trajectories tICA-based dimensionality reduction and data preparation MSM construction and free-energy surface analysis These materials were used in the analysis presented in the following preprint: Seki, T., Ohunuki, J., Okazaki, K.-I., "Conformational Dynamics of Na-Pumping NADH-Quinone Oxidoreductase during Na+ Translocation from AlphaFold-Facilitated Markov State Modeling," preprint, 2026. https://doi.org/10.64898/2026.01.28.702413 This release (v1) fixes the exact versions of scripts and datasets used for the reported results. For detailed instructions on running the analysis and directory structure, see README.md in the repository.