A lightweight Flask-based web interface that automates a full GROMACS molecular-dynamics workflow — from structure preparation to production runs.
• Upload .pdb, .gro, or .g96 structure files
• Choose force field, water model, box type, and ion type
• Automatically runs: pdb2gmx → editconf → solvate → grompp/genion → mdrun
• Includes example .mdp parameter files
• Inspired by Justin A. Lemkul’s GROMACS tutorials
gromacs_gui/
├── app.py
├── input_files/
│ ├── ions.mdp
│ ├── minim.mdp
│ ├── nvt.mdp
│ ├── npt.mdp
│ └── md.mdp
├── static/
│ └── protein.png
├── templates/
│ ├── home.html
│ ├── prep.html
│ └── analyze.html
├── requirements.txt
└── README.md
Python 3.8 +
Flask
GROMACS 2024 + (must be installed and in $PATH)
Install dependencies:
pip install -r requirements.txt
Check GROMACS:
gmx --version
python app.py
Then open http://127.0.0.1:5000 in your browser.
Upload a PDB, choose parameters, and wait for completion.
Results appear in the same directory.
vmd md.tpr md.trr
pymol md.gro
Based on Justin Lemkul’s GROMACS tutorials (https://www.mdtutorials.com/gmx/)
MIT License — free to use and modify with attribution.