waveletswave/hydromd-equilibrate

HydroMD-Equilibrate is a Python tool for determining equilibrium in molecular dynamics simulations using statistical trend analysis with the Mann-Kendall test and Sen's slope estimation.

HydroMD-Equilibrate: Equilibration Analysis in Molecular Dynamics Simulations

Introduction

HydroMD-Equilibrate is a Python-based analytical tool designed to detect equilibrium states in molecular dynamics simulations. Developed during a class exercise, this tool epitomizes the intersection of statistical analysis and physical simulation, reflecting a commitment to interdisciplinary learning and application.

Background

Determining when a molecular system has reached equilibrium is a pivotal step in simulation analysis. By integrating the Mann-Kendall trend test and Sen's slope estimator, HydroMD-Equilibrate offers a novel statistical approach to this challenge, broadening the scope of traditional methods used in the field of molecular dynamics.

Features

• Performs time series analysis to detect equilibration in molecular dynamics simulations.
• Employs the Mann-Kendall test to identify trends within the data.
• Uses Sen's slope estimator to quantify the rate of change and assess stability.
• Pinpoints equilibration points, enhancing the interpretability of simulation results.

Requirements

• Python 3.x
• NumPy
• pymannkendall
• matplotlib

Installation

Clone the repository to your local machine for easy access and updates:

git clone https://github.com/waveletswave/HydroMD-Equilibrate.git

Usage

Execute the HydroMD-Equilibrate script to process your data:

python HydroMD-Equilibrate.py

The script will output a plot illustrating the temperature trends, equilibration points, and Sen's slope, providing a visual cue for equilibrium detection.

Visualization

Below is an example output from HydroMD-Equilibrate, showcasing temperature data versus time, with equilibration points and Sen's slope highlighted:

Contributing

Contributions are welcome! Whether you are a seasoned researcher or a student exploring molecular dynamics, your insights can help enhance HydroMD-Equilibrate. We value a culture of collaboration and open dialogue across disciplines.

License

This project is open-source and available under the MIT License.

Acknowledgments

This tool is a product of academic curiosity and interdisciplinary dialogue. Special thanks to the academic community for fostering an environment where such cross-pollination of ideas is encouraged.