# Molecular Dynamics Tutorial for Beginners

This site hosts interactive notebooks for a beginner-friendly Molecular Dynamics (MD) course.

Use the launch buttons at the top of each page to run notebooks on Binder.

## About This Course
- Audience: beginners starting MD from first principles.
- Style: concept-first explanations with runnable notebook examples.
- Tooling: Python, NumPy, Matplotlib, and ASE-based demonstrations.
- Goal: build intuition first, then introduce practical enhanced-sampling workflows.

## How To Use The Site
1. Start from Module 1 and go in order.
2. Read the markdown explanations first, then run code cells.
3. For interactive execution online, use Binder launch buttons on each page.
4. If a notebook is computationally heavy, use the notebook's fast-mode settings (where available).

## Course Modules
- 1. Introduction to MD
- 2. Physics of MD
- 3. Non-bonded interactions
- 4. 1D simulations
- 5. Sampling challenge and CVs
- 6. Umbrella sampling and WHAM
- 7. Metadynamics
- 8. ASE LJ fluid simulation

## Attribution
This tutorial is done by **Suman Saha** (with the help of **GPT-5.3-codex**).

If you find any bug or in-correction, please report it to [24.sumansaha@gmail.com](mailto:24.sumansaha@gmail.com).