Molecular Dynamics Tutorial for Beginners

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

    1. Physics of MD

    1. Non-bonded interactions

    1. 1D simulations

    1. Sampling challenge and CVs

    1. Umbrella sampling and WHAM

    1. Metadynamics

    1. 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.

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