Tutorials

In addition to reading the documentation, we have prepared several examples to highlight the usage and capabilities of PyRETIS. The cards below point to the user-facing tutorial folders that ship with the source tree. Larger published-result packages that regenerate figures from validation studies are collected on the results page. The complete tutorial list is in the example section.

The examples below are grouped by what you are most likely to change: the potential, the sampling method, the external dynamics engine, or the molecular dynamics workflow. Each card links to the rendered documentation and to the matching source folder under examples/tutorials/.

Start here

A minimal input file

The shortest input that runs a complete RETIS simulation – only the physics, everything else defaulted.

Tutorial source

Minimal, external engine

The same, driving OpenMM: the engine owns the system, so the input is only what to sample and how to measure it.

Tutorial source

Potentials

1D double well

The smallest TIS/RETIS model: one particle in the van Erp double-well benchmark.

Tutorial source

1D triple well

RETIS on a three-state landscape, including the zero_left shortcut for the [0-] ensemble.

Tutorial source

2D hysteresis

A two-dimensional internal potential where the best order parameter is deliberately less obvious.

Tutorial source

2D WCA bond

Bond breaking in the WCA model from van Erp, Moroni and Bolhuis (2003), with low- and high-barrier variants.

Tutorial source

Sampling methods

TIS and flux

Initial flux plus TIS crossing probabilities for the 1D double-well system.

Tutorial source

RETIS

Replica exchange between path ensembles for the same double-well benchmark.

Tutorial source

Infinite swapping

Asynchronous, parallel replica exchange driven by the [runner] worker pool – the route for large rate-constant runs.

Tutorial source

Subtrajectory moves

Stone skipping, web throwing and wire fencing from Riccardi et al. (2017) and Zhang et al. (2023).

Tutorial source

Umbrella sampling

Monte Carlo umbrella sampling for free-energy estimation alongside the rate-constant tutorials.

Tutorial source

Permeability

A path-sampling setup using permeability = true in [simulation] for membrane-style transport calculations.

Tutorial source

Particle swarm

Use the PyRETIS library for a task it is not built for: particle-swarm optimisation of the Ackley function, with a new potential and a new engine.

Tutorial source

REPPTIS

Replica-exchange partial-path TIS on the 1D double well, with the Markov-state-model kinetics analysis.

Tutorial source

Both rates in one run

Bidirectional RETIS on an asymmetric double well: the rates of A to B and of B to A, and the equilibrium constant, from one simulation.

Tutorial source

Exploring the landscape

Free-energy landscape exploration to generate a first valid initial path before path sampling.

Tutorial source

External engines

GROMACS

Methane transport in an sI hydrate structure with a custom Python order parameter.

Tutorial source

LAMMPS

The 2D WCA bond-breaking model driven by LAMMPS instead of the internal engine.

Tutorial source

CP2K

A small hydrogen bond-breaking example using CP2K for the dynamics.

Tutorial source

OpenMM

RETIS for an argon model with OpenMM providing the molecular dynamics.

Tutorial source

Compiled extensions

C and FORTRAN extensions for custom integrators, potentials and order parameters.

Tutorial source

Molecular dynamics

pyretis run MD

Plain molecular dynamics from an input file and from the PyRETIS Python API.

Tutorial source

Extending with C/FORTRAN

This example shows how we can use FORTRAN or C to speed up PyRETIS calculations: a Lennard-Jones mixture is run forward, then with its velocities reversed.

Tutorial source