MD-playground: A Minimal Molecular Dynamics Engine in Python

About

MD-playground is a Python-based molecular dynamics (MD) simulation engine designed for simplicity and extensibility. The engine is capable of simulating:

• Simulations of single particles in various potentials.
• Dynamics in both NVE (microcanonical) and NVT (canonical) ensembles.
• Advanced enhanced sampling techniques like Metadynamics.

Key Features

• Integrators:
  • Velocity Verlet for time integration.
• Thermostats:
  • Optional temperature control for NVT ensemble.
• Potentials:
  • Predefined potentials, including Harmonic and Double-Well.
• Enhanced Sampling:
  • Metadynamics to accelerate rare event sampling.

Getting Started

Installation

Clone the repository:

git clone https://github.com/mandal13/MD-playground.git
cd MD-playground

Example Simulation

Run the simulation with:

python main.py --animation --potential double_well --positions 1.75 --save_file animation.mp4
ffmpeg -i animation.mp4 -vf "fps=30,scale=640:-1:flags=lanczos" animation.gif