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PyRETIS

PyRETIS is Python software for rare-event molecular simulation, path

Their llms.txt

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# 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.

AI agents working with PyRETIS start at **Agent-TIS**
(https://www.pyretis.org/dev/user/agent-tis.html): the user skill
(set up, run and analyse path-sampling simulations) and the developer skill
(extend and validate the code), with the rules for agents and model choice.

## Core Links

- Develop documentation: https://www.pyretis.org/dev/
- Agent-TIS, AI agents for PyRETIS: https://www.pyretis.org/dev/user/agent-tis.html
- Stable PyRETIS 3.0.6 documentation: https://www.pyretis.org/current/
- Full documentation text in one file: https://www.pyretis.org/dev/llms-full.txt
- Source repository: https://gitlab.com/pyretis/pyretis
- License: https://www.pyretis.org/dev/about/license.html

## User Documentation

- [Agent-TIS: AI agents for PyRETIS path sampling](https://www.pyretis.org/dev/user/agent-tis.html): Agent-TIS: run and develop PyRETIS path-sampling simulations (TIS, RETIS, REPPTIS) with AI agents. Agent skills, llms.txt, rules, model choice.
- [The PyRETIS analysis application](https://www.pyretis.org/dev/user/analyse.html): The PyRETIS analysis application, pyretis analyse, is used to analyse the results from PyRETIS simulations.
- [The PyRETIS application](https://www.pyretis.org/dev/user/application.html): PyRETIS ships a single command, pyretis, with sub-commands:
- [Cleaning run artifacts](https://www.pyretis.org/dev/user/clean.html): A PyRETIS run leaves a number of generated files and directories behind – log files, the regenerated out.toml / out.rst, restart files, the NNN ensemble…
- [Creating custom engines](https://www.pyretis.org/dev/user/engine.html): The Engines are used to propagate the equations of motion or alter the state of the system in some other way.
- [Some common PyRETIS errors](https://www.pyretis.org/dev/user/errors.html): In this section, we describe some of the most common PyRETIS warning or error messages and how these errors can be resolved.
- [CECAM workshop: A single particle in a 1D potential](https://www.pyretis.org/dev/user/exercises/examples-cecam-2016.html): This is a short user guide for running the 1D potential example with the RETIS algorithm for the CECAM school “Multiscale Simulations of Soft Matter with…
- [Molecular modelling: Introduction to RETIS](https://www.pyretis.org/dev/user/exercises/examples-molmod-2016.html): In this exercise, you will explore a rare event with the Replica Exchange Transition Interface Sampling (RETIS) algorithm.
- [PyRETIS exercises](https://www.pyretis.org/dev/user/exercises/index.html): Here, we list s
…

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