/GROMACS-simulation-examples

Primary LanguageJupyter Notebook

GROMACS Simulation Repository

This repository contains a collection of Jupyter Notebooks, simulation files, and analysis tools for molecular dynamics simulations conducted using GROMACS. These resources are primarily aimed at educational and demonstration purposes, particularly for sharing simulation workflows and results.

T cell receptor (TCR) Simulation https://www.youtube.com/watch?v=COYKtf-2fC8

Porcine Circovirus single stranded DNA all-atom simulation https://www.youtube.com/watch?v=BsK3dr4lPrw

Lysozyme Simulation https://www.youtube.com/watch?v=Q2OYA0dTxJU

Repository Contents

  • Jupyter Notebooks: Step-by-step guides and scripts for running and analyzing molecular dynamics simulations.
  • PDB Files: Protein Data Bank files that contain the 3D structures of proteins used in the simulations.
  • GRO Files: GROMACS structure files, detailing the system setup for simulations.
  • ITP Files: Include Topology files used by GROMACS for defining non-standard molecules.
  • MDP Files: Molecular Dynamics Parameter files that specify the simulation parameters.
  • NVT Files: Files related to the canonical ensemble (constant Number of particles, Volume, and Temperature) simulations.
  • NDP Files: Typically, these should refer to simulation setup files; ensure correct file type specifications as needed.
  • XTC Files: Compressed trajectory files that store the coordinates of the atoms throughout the simulation.

Tools Used

  • GROMACS: Open-source software for high-performance molecular dynamics, primarily designed for biochemical molecules.
  • MDAnalysis: A Python library that simplifies the analysis of molecular dynamics trajectories and protein structures. Used in the Jupyter Notebooks for detailed analysis.

How to Use This Repository

To use the materials in this repository, follow these steps:

  1. Clone the Repository:

    git clone https://github.com/yourusername/gromacs-simulation-repository.git

  2. Set Up Your Environment:

    • Ensure you have Python installed along with Jupyter. Installation of GROMACS on your system is required to run simulations.
    • Install MDAnalysis: 
      pip install MDAnalysis

  3. Running the Notebooks:

    • Navigate to the directory containing the cloned repository.
    • Start Jupyter Notebook: 
      jupyter notebook
    • Open the desired notebook and follow the instructions within.

Purpose of This Repository

This repository serves as a showcase for my skills in molecular dynamics simulation and analysis, contributing to my portfolio in the fields of computational biology and computational drug and protein design. The simulations and analyses detailed here reflect my ongoing learning process and my commitment to contributing to scientific and medical research through computational methods.

Connect with Me

  • LinkedIn:

Feel free to reach out for collaborations or discussions!