PolyzyMD Documentation

PolyzyMD is a molecular dynamics simulation toolkit for studying enzyme-polymer systems. It provides a streamlined workflow for setting up, running, and managing MD simulations on HPC clusters.

Note

PolyzyMD is under active development. If you encounter issues, please open an issue on GitHub.

Features

YAML-based Configuration: Define your entire simulation in a single, validated config file
Automated System Building: Combine enzymes, substrates, polymers, and solvents
HPC Integration: Self-resubmitting SLURM jobs with automatic checkpointing and recovery
Flexible Restraints: MDAnalysis-style atom selection for distance restraints
OpenFF/OpenMM Backend: Modern force fields and GPU-accelerated simulations

Quick Example

name: "LipA_polymer_simulation"

enzyme:
  name: "LipA"
  pdb_path: "structures/enzyme.pdb"

polymers:
  enabled: true
  type_prefix: "SBMA-EGPMA"
  monomers:
    - label: "A"
      probability: 0.98
      name: "SBMA"
    - label: "B"
      probability: 0.02
      name: "EGPMA"
  length: 5
  count: 2

 simulation_phases:
   production:
     duration: 100.0  # ns

# Validate and submit
polyzymd validate -c config.yaml
polyzymd submit -c config.yaml --replicates 1-5 --preset aa100

Getting Started

Tutorials

API Reference

API Documentation

Indices and tables