AGENTS.md
CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
SECURITY.md
SUPPORT.md
mkdocs.yml
pyproject.toml
bff/__init__.py
bff/cli.py
bff/gromacs.py
bff/plotting.py
bff/slurm.py
bff/topology.py
bff/bayes/__init__.py
bff/bayes/effective_observations.py
bff/bayes/fit.py
bff/bayes/gaussian_process.py
bff/bayes/kernels.py
bff/bayes/learning.py
bff/bayes/likelihoods.py
bff/bayes/means.py
bff/bayes/posterior.py
bff/bayes/priors.py
bff/bayes/results.py
bff/bayes/utils.py
bff/domain/__init__.py
bff/domain/bias.py
bff/domain/charge_constraints.py
bff/domain/samples.py
bff/domain/specs.py
bff/domain/systems.py
bff/io/__init__.py
bff/io/colvars.py
bff/io/commands.py
bff/io/logs.py
bff/io/mdp.py
bff/io/plumed.py
bff/io/progress.py
bff/io/utils.py
bff/mcmc/__init__.py
bff/mcmc/convergence.py
bff/mcmc/proposal.py
bff/mcmc/sampler.py
bff/qoi/__init__.py
bff/qoi/analysis.py
bff/qoi/dataset.py
bff/qoi/hbonds.py
bff/qoi/rdf.py
bff/qoi/routines.py
bff/qoi/trajectory.py
bff/workflows/__init__.py
bff/workflows/config.py
bff/workflows/examples.py
bff/workflows/build/__init__.py
bff/workflows/build/box.py
bff/workflows/build/config.py
bff/workflows/build/main.py
bff/workflows/build_qoi_datasets/__init__.py
bff/workflows/build_qoi_datasets/config.py
bff/workflows/build_qoi_datasets/main.py
bff/workflows/campaign/__init__.py
bff/workflows/campaign/config.py
bff/workflows/campaign/job.py
bff/workflows/campaign/run.py
bff/workflows/fit_lgp/__init__.py
bff/workflows/fit_lgp/config.py
bff/workflows/fit_lgp/main.py
bff/workflows/learn/__init__.py
bff/workflows/learn/config.py
bff/workflows/learn/main.py
bff/workflows/sample_parameters/__init__.py
bff/workflows/sample_parameters/config.py
bff/workflows/sample_parameters/main.py
bff/workflows/validate/__init__.py
bff/workflows/validate/config.py
bff/workflows/validate/main.py
bfflearn.egg-info/PKG-INFO
bfflearn.egg-info/SOURCES.txt
bfflearn.egg-info/dependency_links.txt
bfflearn.egg-info/entry_points.txt
bfflearn.egg-info/requires.txt
bfflearn.egg-info/top_level.txt
docs/changelog.md
docs/cli.md
docs/development.md
docs/index.md
docs/installation.md
docs/migration.md
docs/reference-trajectories.md
docs/results.md
docs/workflow.md
docs/assets/bff-logo.pdf
docs/assets/bff-logo.svg
docs/configuration/build-qoi-datasets.md
docs/configuration/build.md
docs/configuration/fit-lgp.md
docs/configuration/index.md
docs/configuration/learn.md
docs/configuration/sample-parameters.md
docs/configuration/validate.md
docs/configuration/snippets/campaign-options.md
docs/examples/acetate.md
docs/examples/arbitrary-data.md
docs/examples/index.md
docs/examples/neon-mie-lgpmd.md