Examples

The examples directory contains runnable notebooks covering simulations and optimizations.

When experimenting with the notebooks, be sure to read the examples README, including the prequisites section to ensure you have the necessary software and access to example data.

Simulations

Notebook	Backend	Description
simulation.ipynb	JAX-MD	Run a DNA simulation entirely in JAX with Langevin dynamics.
simulation.ipynb	oxDNA	Run an oxDNA simulation and read back the trajectory.
bottom_up_optimization.ipynb	GROMACS	Run a GROMACS-based MARTINI workflow (includes simulation + analysis).

Optimizations

Simple (direct differentiation)

Notebook	Backend	Description
propeller_twist_optimization.ipynb	JAX-MD	Optimize stacking parameters against propeller twist via autodiff.

Advanced (DiffTRe / multi-objective)

Notebook	Backend	Description
propeller_twist_optimization.ipynb	oxDNA	Single-trajectory DiffTRe optimization of stacking parameters.
multi_trajectory_optimization.ipynb	oxDNA	Multi-trajectory DiffTRe optimization with Ray parallelism.
persistence_length_optimization.ipynb	oxDNA	Persistence length optimization using DiffTRe.
melting_temperature_optimization.ipynb	oxDNA	Melting temperature optimization with umbrella sampling.
lammps_propeller_twist_optimization.ipynb	LAMMPS	oxDNA model optimization using the LAMMPS backend.
bottom_up_optimization.ipynb	GROMACS	Bottom-up Martini M2 fitting via Wasserstein distance matching.
membrane_thickness_optimization.ipynb	GROMACS	Membrane thickness optimization for Martini M2.
melting_temperature_optimization.ipynb	GROMACS	Melting temperature optimization for Martini M3 with Ray.