Get Started

Welcome to PolyzyMD! This page gets you from zero to a working setup in about 10 minutes.

Quick Install

PolyzyMD uses pixi for environment management. Install pixi (if you don’t already have it), then clone and set up the project:

# Install pixi
curl -fsSL https://pixi.sh/install.sh | sh
source ~/.bashrc

# Clone and install PolyzyMD
git clone https://github.com/joelaforet/polyzymd.git
cd polyzymd
pixi install -e build
pixi shell -e build

Verify the install:

polyzymd --help
polyzymd info

If both commands print output without errors, you are ready to go.

For the full installation guide (including GPU cluster setup and troubleshooting), see Install PolyzyMD with pixi.

Create Your First Project

PolyzyMD organizes simulations into project directories. Create one with:

polyzymd init --name my_first_project
cd my_first_project

This creates a directory with a template config.yaml, a structures/ folder for your input PDB files, and job_scripts/ and slurm_logs/ directories for HPC workflows.

What’s Inside `config.yaml`

The config.yaml file controls everything about your simulation: which enzyme to simulate, solvent conditions, thermodynamic parameters, equilibration stages, and production settings. You edit this file to describe your system, then PolyzyMD handles the rest.

For a detailed walkthrough of writing your first config and running a build, see Run Your First PolyzyMD Simulation.