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PolyzyMD Documentation

PolyzyMD is a molecular dynamics toolkit for building, running, and analyzing enzyme-polymer simulations.

Use this site by need:

  • Start here if you need to install PolyzyMD or run a first simulation.

  • Use Tutorials for guided, end-to-end learning.

  • Use How-To Guides for specific tasks such as SLURM submission, restraints, polymers, GROMACS export, or condition comparisons.

  • Use Reference for command lookup, configuration details, benchmarks, and API docs.

  • Use Explanation for concepts, rationale, interpretation, and best practices.

  • Use Contributor Guide for development architecture and extension workflows.

Note

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

Note

Stable analysis workflows for the v1.2.0 release are RMSF, contacts, distances, catalytic triad, and secondary structure. Binding preference, exposure dynamics, binding free energy, and polymer affinity remain available, but are documented as experimental.

Choose Your Path

  • Get Started Install PolyzyMD with pixi and run your first simulation.

  • Tutorials Follow guided, end-to-end workflows with clear success states.

  • How-To Guides Solve a specific task quickly without wading through background material.

  • Reference Look up commands, config schema, API modules, and benchmark data.

  • Explanation Understand why workflows are structured the way they are and how to interpret results.

  • Contributor Guide Extend PolyzyMD, understand the architecture, and contribute safely.

Common Workflows

Indices and Tables