🌟 Molecular Dynamics Simulations Resources 🌟

Welcome to this collection of resources for Molecular Dynamics (MD) simulations! Whether you're looking for theory, tutorials or tools for analysis and visualisation, we've got you covered. Let's explore the fascinating world of computational biology and MD simulations together!

📚 Literature and Tutorials

• Complete Theory and Tutorials with OpenMM + Jupyter Notebooks
  Check out CHEM101.6 by Paul Robustelli for an in-depth guide on MD simulations with OpenMM and Jupyter.

• Molecular Modeling Principles and Applications (Complete Book)
  Get your hands on this Molecular Modeling Book for comprehensive learning.

• MD Theory and Tutorials
  A great resource for MD theory and tutorials: OpenCADD MD Tutorials.

• Review on MD and Docking
  A fantastic review article on MD and docking to understand the synergy between these two techniques.

• MD Theory and exercise
  Learn the fondumental theory and rules behind MD simulation: Practical considerations for Molecular Dynamics

🎥 Video Lessons

• Prof. Erik Lindahl's Complete Course
  Dive into the world of molecular simulations and computational biophysics with Erik Lindahl on youtube. So much knowledge packed in there!

• VMD for Dummies - Dr. Mohamed Shehata's Complete Course
  Learn step by step all the basics of VMD to study, visualize, and analyze MD trajectories with the VMD Complete Course on YouTube.

📝 MD package tutorials

• GROMACS Tutorials
  Need help with system building and simulations in GROMACS? The GROMACS tutorials have you covered.

• Amber Tutorials
  One of the most comprehensive tutorials out there! Get started with Amber Tutorials.

• HTMD Tutorials
  From rudimentary Python to system building and MD simulations, the HTMD tutorials are a great place to start!

🛠️ Tools for MD Analysis

• R for Bio3D
  Check out Bio3D - The Grant Lab for amazing tools and resources for structural bioinformatics.

• MDAnalysis (Python)
  Analyze your MD simulations with MDAnalysis, a powerful Python library.

• MDtraj
  A great Python library for analyzing MD simulations: MDtraj.

• Plumed
  Want to dive into analysis and enhanced sampling? Plumed is your go-to tool.

• AmberTools
  Explore AmberTools for additional analysis and simulation tools from the Amber suite.

• ProDy
  Another great resource for protein structural dynamics: ProDy.

⚙️ MD Engines

• GROMACS (Bash Command Line)
  GROMACS is a powerful tool for MD simulations with command-line interfaces.

• OpenMM (Python)
  Run your MD simulations with the ease of Python using OpenMM.

• ACEMD (Free for one GPU)
  A highly efficient MD engine. Get started with ACEMD.

• AMBER (Small fee for academics – one-time payment)
  Explore the capabilities of AMBER, a top-tier MD simulation suite.

• CHARMM
  The classic MD engine! Learn more about CHARMM.

• CHARMM-GUI (System and Input Generation for MD)
  Get a helping hand in setting up your MD simulations with CHARMM-GUI.

• Desmond (Schrödinger) (Paid)
  Learn more about Desmond, another powerful MD engine.

🤖 AI-Based Software for Conformational Ensemble Generation

• Curated list
  AI-powered tools and software used to generate conformational ensembles in molecular modeling and structural biology. Link

🖥️ Visualization/Render Software

• VMD
  Visualize and analyze molecular dynamics simulations with VMD.

• PyMOL
  A popular tool for visualization and rendering: PyMOL.

• ChimeraX
  Dive into molecular visualizations with ChimeraX.

• Bioblender
  Render of 3D protein and MD trajectories Bioblender.

• Bioblender Crash Course for Biochemists - Brady Johnston
  Introductory videos on how Bioblender works and how to handle cutting-edge protein rendering and visualize your MD trajectory close to reality. Check out the Bioblender Crash Course on YouTube, and here’s more on How Molecular Nodes Work.

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Happy simulating and exploring! 😄 Whether you're new to molecular dynamics or a seasoned pro, these resources will help you take your skills to the next level! 🚀

🔨 This collection is updated to include the latest materials and tutorials. Contributions and suggestions are always welcome!

🧬 The emoji used in this README is sourced from the protein-emoji repository by Andrew White.