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Gorgona: a python-based tool for intestinal environment simulations with lammps

The simulation tool was developed within T3.6 of the 3D'omics project.

Gorgona workflow

To install Gorgona:

  1. Clon this repo locally
  2. Create a conda environment based on the provided environment.yml file: conda env create -f environment.yml
  3. Activate the environment: conda activate gorgona
  4. Install Gorgona by running pip install -e .

Follow Jupyter notebooks in the folder examples to run Gorgona on the example input data. For LAMMPS and OVITO installation instructions see INSTALL.md.