Installation

Requirements

• Python 3.11 or higher
• pixi (recommended) or conda/mamba
• Git

Install from source

git clone https://github.com/emdgroup/mdfactory.git
cd mdfactory

pixi install

conda create -n mdfactory -c conda-forge python rdkit \
    openff-toolkit openff-interchange openff-nagl openff-units openmm
conda activate mdfactory
pip install -e .

Development installation

If you plan to contribute or modify the code, install development tooling:

With pixi:

pixi run -e dev test

The dev environment includes testing and linting tools.

Without pixi:

conda activate mdfactory
pip install -e .[dev]

Verify installation

Check that MDFactory is installed correctly:

python -c "import mdfactory; print(mdfactory.__version__)"

Then verify the CLI:

pixi run mdfactory --help

Or without pixi (with the conda environment activated):

mdfactory --help

MD engine dependencies

MDFactory currently supports GROMACS workflows with OpenMM-assisted build steps.

GROMACS

conda install -c conda-forge gromacs

OpenMM

conda install -c conda-forge openmm

LAMMPS support is on the roadmap and is not currently supported in the active workflows.

Optional components

Submitit for SLURM analysis jobs

pip install "mdfactory[submitit]"

Foundry integration

pip install "mdfactory[foundry]"

The interactive Foundry setup also expects the fdt command to be available on PATH.

CGenFF

If you use parametrization: cgenff, configure the SilcsBio install path in your config file (typically ~/.config/mdfactory/config.ini):

[cgenff]
SILCSBIODIR = /path/to/silcsbio

Next steps