OpenFreeEnergy/feflow

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Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits

Stars: 20
Forks: 4
Open beginner issues: 0
Indexed issues: 45

Dominant language: Python
License: MIT
Last GitHub push: Jul 7, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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45 open issues indexed

Testing HTF end states for protein mutation Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

OpenFreeEnergy/feflow#134 · Opened Dec 18, 2025
Fix/recover self-hosted GPU CI Open

OpenFreeEnergy/feflow#126 · 2 comments · 1 assignee · Opened Aug 21, 2025
data.py clean-up Open

OpenFreeEnergy/feflow#122 · 1 assignee · Opened Jun 27, 2025
Improve exception handling for protein mutations Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#121 · 1 comment · Opened Jun 27, 2025
Protein Mutation Mapping fails on Complex Phase using Apo Mapping JSON file Open

OpenFreeEnergy/feflow#120 · 1 comment · 1 reaction · 1 assignee · Opened Jun 16, 2025
Community: Protein Mutations Open

openfe

Difficulty 5/5 Over a week Newbie friendliness 10/100

OpenFreeEnergy/feflow#119 · Opened Jun 1, 2025
Detect when the transformation is the same and output zero as the FE estimate Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#108 · Opened Feb 11, 2025
Add API docs and a userguide Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#107 · Opened Jan 31, 2025
Speeding up the HTF Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#105 · 4 comments · Opened Jan 7, 2025
Add `num_cycle_laps` setting to `NonEquilibriumCyclingProtocol`, allowing for additional NEQ iterations within each `CycleUnit` Open

OpenFreeEnergy/feflow#102 · 9 comments · 1 assignee · Opened Dec 12, 2024
Modularize parameterization, joining topologies and creating systems Open

OpenFreeEnergy/feflow#101 · 7 comments · 1 assignee · Opened Dec 11, 2024
Utility functions to acquire components in a system Open

OpenFreeEnergy/feflow#100 · 1 comment · 1 assignee · Opened Dec 11, 2024
Checking states compatibility Open

OpenFreeEnergy/feflow#99 · 1 assignee · Opened Dec 11, 2024
Add tests for different solvent box types for NECycling Protocol Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#91 · Opened Sep 26, 2024
Fail when multiple alchemical components are detected Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#83 · Opened Sep 16, 2024
Atom shifting mapping for protein mutations Open

OpenFreeEnergy/feflow#82 · 1 assignee · Opened Sep 16, 2024
Test insertion codes Open

OpenFreeEnergy/feflow#81 · 3 comments · 1 assignee · Opened Sep 16, 2024
Create a ProteinMapping subclass Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#74 · 1 comment · Opened Sep 16, 2024
Add duecredit Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

OpenFreeEnergy/feflow#71 · Opened Sep 13, 2024
Support for different protein conformations in the protocol Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

OpenFreeEnergy/feflow#69 · 1 comment · Opened Sep 12, 2024
Try to document where the protocols are useful in projects Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#68 · Opened Sep 12, 2024
Create test TestNonequilibriumCyclingProtocol that uses Gaussian random numbers to quickly generate analyzable test data Open

component-protocol

Difficulty 4/5 3-5 days Newbie friendliness 45/100

OpenFreeEnergy/feflow#67 · Opened Sep 11, 2024
`NonEquilibriumCyclingProtocol` : Add ability to have multiple iterations/laps within a single `CycleUnit`? Open

component-protocol enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

OpenFreeEnergy/feflow#66 · 1 comment · Opened Sep 11, 2024
Implement NEq switching by transforming current NEq Cycling Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#65 · Opened Sep 4, 2024
Failing `test_unsampled_endstate_energies_GPU` test Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#63 · Opened Aug 27, 2024
Add systems, components and mapping validation when creating a protocol Open

enhancement

OpenFreeEnergy/feflow#54 · 1 assignee · Opened Jul 26, 2024
Stabilize settings before release Open

OpenFreeEnergy/feflow#51 · 1 assignee · Opened Jul 1, 2024
Allow passing a `json` file for forcefield parameters cache Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#50 · 1 comment · Opened Jun 25, 2024
Test against lastest OpenFF release instead of GAFF Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#48 · Opened Jun 4, 2024
refactor HTF `softcore_LJ` to understand literals instead of bools Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#42 · 1 reaction · Opened Mar 24, 2024
[NEQCycling] User defined LocalEnergyMinimizer steps Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#41 · Opened Mar 19, 2024
Enable settings for choosing partial charge generation method Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

OpenFreeEnergy/feflow#39 · Opened Mar 13, 2024
Setup Unit should work with different integrators Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#36 · Opened Mar 9, 2024
Integrate code formatting pre-commit hooks in CI Open

enhancement

OpenFreeEnergy/feflow#34 · 1 assignee · Opened Mar 6, 2024
Not requiring perses for testing hybrid topology implementation Open

enhancement testing

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#30 · Opened Feb 29, 2024
Miscellaneous HTF improvements Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#29 · 1 comment · Opened Feb 27, 2024
Protocol : Times Square Sampling Open

component-protocol

Difficulty 5/5 Over a week Newbie friendliness 30/100

OpenFreeEnergy/feflow#25 · Opened Jan 31, 2024
Migrate openmm specific settings from upstream Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/feflow#22 · Opened Dec 13, 2023
Add duecredit support Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#18 · Opened Dec 4, 2023
Add user selection of charge backends Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

OpenFreeEnergy/feflow#17 · Opened Nov 28, 2023
Implement ATM protocol Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#15 · Opened Nov 28, 2023
Integrate REST capable HTF from perses into FEflow Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

OpenFreeEnergy/feflow#8 · 1 comment · Opened Nov 6, 2023
Alchemical settings migration Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/feflow#6 · 1 reaction · Opened Oct 13, 2023
Extend protocols results with helpful quantities for analysis Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

OpenFreeEnergy/feflow#5 · 2 comments · Opened Oct 10, 2023
Add `extends` support to the `NonEquilibriumCyclingProtocol` Open

priority:medium

OpenFreeEnergy/feflow#2 · 1 comment · 2 assignees · Opened Sep 27, 2023

OpenFreeEnergy/feflow

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