Installation

Local installation

conda create -n martinisurf python=3.11 -y
conda activate martinisurf
pip install -r requirements.txt
pip install -e .

External tools required

• martinize2 for protein mode

• Python 2.7 for DNA mode (martinize-dna.py)

• GROMACS (gmx or gmx_mpi) for solvation/ionization and simulation runs

Quick checks

which martinisurf
which martinize2
which gmx
python2.7 -V

Build docs locally

pip install -r docs/requirements.txt
sphinx-build -b html docs docs/_build/html

Then open docs/_build/html/index.html.