Molecular dynamics simulation toolkit for enzyme-polymer systems.
Documentation • Installation • Quick Start
PolyzyMD provides a streamlined workflow for setting up and running MD simulations of enzymes with co-polymer chains. It handles:
- System Building: Combine enzyme structures, docked substrates, and random co-polymers
- Solvation: Add water, ions, and optional co-solvents with PACKMOL
- Simulation: Run equilibration and production with OpenMM
- HPC Integration: Daisy-chain job submission for SLURM clusters
- Configuration: YAML-based configuration with validation
PolyzyMD requires OpenMM and the OpenFF stack, which are only available via conda/mamba.
Step 1: Create conda environment
Using mamba (recommended for speed):
mamba create -n polyzymd-env python=3.11 openmm openff-toolkit openff-interchange \
openff-nagl openff-nagl-models openff-forcefields openff-units packmol \
mbuild mdtraj numpy scipy pandas pydantic pyyaml click tqdm -c conda-forge
mamba activate polyzymd-envOr using our environment file:
mamba env create -f https://raw.githubusercontent.com/joelaforet/polyzymd/main/devtools/conda-envs/polyzymd-env.yml
mamba activate polyzymd-envStep 2: Install PolyzyMD
pip install polyzymdFor contributing or modifying the source code:
git clone https://github.com/joelaforet/polyzymd.git
cd polyzymd
mamba env create -f devtools/conda-envs/polyzymd-env.yml
mamba activate polyzymd-env
pip install -e ".[dev]"Note for uv users: OpenMM and the OpenFF stack are not available on PyPI and must be installed via conda/mamba. You can use uv for other packages within an activated conda environment, but the core simulation dependencies require conda.
For detailed installation instructions, including HPC setup and troubleshooting, see the Installation Guide.
polyzymd init --name my_simulation
cd my_simulationThis creates a project directory with a template config.yaml and placeholder files.
cp /path/to/enzyme.pdb structures/
cp /path/to/substrate.sdf structures/ # optional# Edit config.yaml with your settings, then:
polyzymd validate -c config.yaml
polyzymd submit -c config.yaml --replicates 1-5 --preset aa100See the Quick Start Guide for a complete walkthrough.
| Command | Description |
|---|---|
polyzymd init -n my_project |
Initialize a new project directory |
polyzymd validate -c config.yaml |
Validate configuration file |
polyzymd build -c config.yaml |
Build simulation system |
polyzymd run -c config.yaml |
Run simulation locally |
polyzymd submit -c config.yaml |
Submit daisy-chain jobs to SLURM |
polyzymd continue -w workdir -s 2 |
Continue from previous segment |
polyzymd info |
Show installation information |
Full documentation is available at polyzymd.readthedocs.io.
MIT License - see LICENSE file for details.
If you use PolyzyMD in your research, please cite:
@software{polyzymd,
author = {Laforet Jr., Joseph R.},
title = {PolyzyMD: MD Simulations for Enzyme-Polymer Systems},
year = {2026},
url = {https://github.com/joelaforet/polyzymd}
}