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PyMD-Notebook

Python License Jupyter

PyMD-Notebook is a Jupyter notebook for performing classical molecular dynamics (MD) simulations in Python. It allows users to run MD on a given atomic configuration and analyze the final positions and radial distribution functions (RDF).

Key Features

Molecular Dynamics Simulation

  • Run classical MD simulations starting from a user-provided atomic configuration.
  • Evolve atomic positions over time according to interatomic forces.
  • Supports user-defined simulation parameters (time step, temperature, number of steps, etc.).

Output Analysis

  • Extract final atomic configuration after the MD simulation.
  • Compute radial distribution functions (RDF) to analyze structural properties.

Python Compatibility

  • Developed in Python 3.12.7.
  • Compatible with JupyterLab and Jupyter Notebook.
  • Uses standard scientific libraries: NumPy, Matplotlib, pandas, etc.

Usage

  1. Open the notebook in an editor.
  2. Load an initial atomic configuration.
  3. Set simulation parameters (time step, temperature, number of steps, etc.).
  4. Run the MD simulation.
  5. Inspect the final atomic configuration and plot RDF or other observables.

License

This repository is licensed under the MIT License.