# Dataset Title
LAMMPS Simulation Files Supporting the Study “Molecular Dynamics Study of Hydrogen Bonding in Neutral Alginate”

## DOI
https://doi.org/10.15480/882.15182

## Authors
- Dr. Vasilii Korotenko, TUHH – vasilii.korotenko@tuhh.de – ORCID: 0000-0002-2045-2536
- Dr. Irina Smirnova, TUHH
- Dr. Pavel Gurikov, TUHH

## Date
May 19, 2025

## Version
v1.0 – Initial upload

## Description
This dataset contains LAMMPS simulation input files and Python scripts used for post-processing hydrogen bonding analysis in neutral alginate systems. Scripts were tested with LAMMPS 3Mar2020 and Python 3.10.

## How to Use
1. Run `in.loop1.sh` through `in.loop5.sh` using LAMMPS to generate trajectory data (e.g., in `.lammpstrj` format).
2. Post-processing and hydrogen bond analysis can be performed using external tools such as:

   - **MDAnalysis** – for trajectory parsing, hydrogen bond detection, and distance-based analysis  
   - **ASE (Atomic Simulation Environment)** – for handling atomic coordinates and computing radial distribution functions  
   - **MDTraj** – for calculating hydrogen bond lifetimes, angle distributions, and contact frequencies

All tools were tested with **Python 3.10**. Users are encouraged to implement their own workflows based on the analysis goals and preferred tools.
## License
MIT License

## Citation
Please cite this dataset as:
Korotenko, V., Smirnova, I., Gurikov, P. (2025). LAMMPS Simulation Files Supporting the Study “Molecular Dynamics Study of Hydrogen Bonding in Neutral Alginate”. TUHH Open Research. https://doi.org/10.15480/882.15182