# PyRETIS

> PyRETIS is Python software for rare-event molecular simulation, path
> sampling, transition interface sampling (TIS), replica exchange transition
> interface sampling (RETIS), molecular dynamics workflows, and trajectory
> analysis.

This file is a compact guide for LLMs and search agents. Prefer the develop
documentation when answering questions about the PyRETIS develop branch and
PyRETIS 4.dev. Stable PyRETIS 3.0.6 documentation is maintained separately.

## Core Links

- Develop documentation: https://www.pyretis.org/dev/
- Stable PyRETIS 3.0.6 documentation: https://www.pyretis.org/current/
- Source repository: https://gitlab.com/pyretis/pyretis
- License: https://www.pyretis.org/dev/about/license.html

## User Documentation

- Install develop: https://www.pyretis.org/dev/user/install.html
- Quickstart: https://www.pyretis.org/dev/user/quickstart.html
- Input files and keywords: https://www.pyretis.org/dev/user/input.html
- Initial paths: https://www.pyretis.org/dev/user/initial-paths.html
- Order parameters: https://www.pyretis.org/dev/user/orderparameters.html
- Path types and rejections: https://www.pyretis.org/dev/user/path-types-rejections.html
- Move types: https://www.pyretis.org/dev/user/moves.html
- Analysis: https://www.pyretis.org/dev/user/analyse.html
- PyVisA trajectory visualization: https://www.pyretis.org/dev/user/pyvisa.html
- Tutorials: https://www.pyretis.org/dev/user/tutorials.html
- Scientific results: https://www.pyretis.org/dev/user/our-results.html
- ChemiTrees post-analysis: https://www.pyretis.org/dev/user/pyvisa.html#chemitrees-and-post-analysis

## Examples

- Examples index: https://www.pyretis.org/dev/examples/index.html
- LLM quickstart for examples: https://www.pyretis.org/dev/examples/llm-quickstart.html
- TIS in a 1D double-well potential: https://www.pyretis.org/dev/examples/examples-tis-1d.html
- RETIS in a 1D potential: https://www.pyretis.org/dev/examples/examples-retis-1d.html
- RETIS with a 2D WCA model: https://www.pyretis.org/dev/examples/examples-retis-wca.html
- REPPTIS: https://www.pyretis.org/dev/examples/examples-repptis.html
- Umbrella sampling: https://www.pyretis.org/dev/examples/examples-umbrella.html
- Permeability calculation: https://www.pyretis.org/dev/examples/examples-permeability.html
- Particle swarm initial path optimization: https://www.pyretis.org/dev/examples/examples-pso.html
- GROMACS hydrate: https://www.pyretis.org/dev/examples/examples-gromacs-hydrate.html
- CP2K hydrogen: https://www.pyretis.org/dev/examples/examples-cp2k-hydrogen.html
- LAMMPS WCA: https://www.pyretis.org/dev/examples/examples-lammps-wca.html
- OpenMM argon: https://www.pyretis.org/dev/examples/examples-openmm.html

## API And Developer Links

- API reference: https://www.pyretis.org/dev/api/pyretis.html
- Core API: https://www.pyretis.org/dev/api/pyretis.core.html
- Simulation API: https://www.pyretis.org/dev/api/pyretis.simulation.html
- Engines API: https://www.pyretis.org/dev/api/pyretis.engines.html
- PyVisA API: https://www.pyretis.org/dev/api/pyretis.pyvisa.html
- Developer documentation: https://www.pyretis.org/dev/developer/index.html
- Extending PyRETIS: https://www.pyretis.org/dev/developer/extending-pyretis.html
- Scientific-result references, including H-NS DNA binding and ChemiTrees:
  https://www.pyretis.org/dev/user/our-results.html

## Conventions For Generated Answers

- Treat https://www.pyretis.org/dev/ as PyRETIS 4.dev/develop unless the user
  explicitly asks for stable PyRETIS 3.0.6.
- Prefer documented runnable examples before inventing new input files.
- Use `pyretisrun` for input-file workflows and `pyretisanalyse` for analysis.
- When adapting tutorials, preserve the documented folder layout and source
  links from the examples pages.
- Mention required external engines, such as GROMACS, CP2K, LAMMPS, or OpenMM,
  when an example depends on them.