OpenFreeEnergy/openfe

The Open Free Energy toolkit

Stars: 332
Forks: 56
Open beginner issues: 4
Indexed issues: 398
Avg merge: 5d 19h
Merged PRs (30d): 10

Dominant language: Python
License: MIT
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted

Beginner friendly Everything

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Solvent leg fails with "cutoff distance cannot be greater than half the periodic box size" and `SimulationNaNError` when using `box_shape="dodecahedron"` with `solvent_padding=1.2 nm Open

OpenFreeEnergy/openfe#2200 · 2 assignees · Opened Sep 21, 2026
Boresch restraint search crashes on ligands with three or more fused aromatic rings (`get_aromatic_rings`: `list.remove(x): x not in list`) Open

Difficulty 2/5 Half a day Newbie friendliness 88/100

OpenFreeEnergy/openfe#2199 · 1 comment · 2 assignees · Opened Sep 19, 2026
Add docs for accessing protocol results Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

OpenFreeEnergy/openfe#2198 · 2 assignees · Opened Sep 18, 2026
task status: simple reporting of counts of status types Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

OpenFreeEnergy/openfe#2196 · 1 assignee · Opened Sep 17, 2026
rename orchestration fixture names for clarity Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

OpenFreeEnergy/openfe#2195 · 1 assignee · Opened Sep 17, 2026
GPU test not picking up OE license Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

OpenFreeEnergy/openfe#2194 · 1 assignee · Opened Sep 17, 2026
Test on openmm-8.6 Open

OpenFreeEnergy/openfe#2193 · 1 assignee · Opened Sep 16, 2026
user testing task-based execution Open

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

OpenFreeEnergy/openfe#2192 · 3 assignees · Opened Sep 16, 2026
Structural analysis for ABFEs Open

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

OpenFreeEnergy/openfe#2191 · 1 assignee · Opened Sep 16, 2026
add n_repeats option to task-based setup Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

OpenFreeEnergy/openfe#2190 · 1 assignee · Opened Sep 15, 2026
Retrieve MBAR errors, MBAR overlapping matrix and forward-backward analysis values after RBFE runs Open

OpenFreeEnergy/openfe#2187 · 1 comment · 1 assignee · Opened Sep 14, 2026
Issues with how net charge varies with lambda: non-zero partial charges outside of end states. Open

OpenFreeEnergy/openfe#2181 · 1 assignee · Opened Sep 6, 2026
Document issues with process limits Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

OpenFreeEnergy/openfe#2179 · Opened Sep 1, 2026
add separate CLI command for generating a task db and warehouse from alchemical network Open

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

OpenFreeEnergy/openfe#2165 · 1 assignee · Opened Aug 20, 2026
add results gathering CLI compatible with warehouse Open

OpenFreeEnergy/openfe#2164 · 1 assignee · Opened Aug 20, 2026
improve Warehouse validation Open

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

OpenFreeEnergy/openfe#2162 · Opened Aug 20, 2026
task_db and warehouse construction should use alchemical_network name by default. Open

OpenFreeEnergy/openfe#2161 · 1 assignee · Opened Aug 20, 2026
add additional views and filters for `openfe status` Open

OpenFreeEnergy/openfe#2160 · 1 assignee · Opened Aug 20, 2026
`set_and_check_new_positions` warning isn't very helpful Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

OpenFreeEnergy/openfe#2159 · 1 assignee · Opened Aug 18, 2026
No delta G value produced eventually Open

OpenFreeEnergy/openfe#2130 · 9 comments · 1 assignee · Opened Aug 10, 2026
worker-based execution: add basic results gathering support Open

OpenFreeEnergy/openfe#2119 · 1 assignee · Opened Aug 3, 2026
Change default partial charge protocol settings to be "from force field" Open

OpenFreeEnergy/openfe#2117 · 1 assignee · Opened Jul 31, 2026
Add validation for partial charge assignment in Protocols Open

OpenFreeEnergy/openfe#2115 · 2 assignees · Opened Jul 31, 2026
Extensions: warehouse adaptations Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

OpenFreeEnergy/openfe#2107 · Opened Jul 27, 2026
SepTop multi-extension suppport Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

OpenFreeEnergy/openfe#2106 · Opened Jul 27, 2026
AFEs multi-extensions support Open

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

OpenFreeEnergy/openfe#2105 · Opened Jul 27, 2026
HybridTop multi-extension support Open

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

OpenFreeEnergy/openfe#2104 · Opened Jul 27, 2026
HybridTop single extension support Open

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

OpenFreeEnergy/openfe#2103 · Opened Jul 27, 2026
Extensions: CLI updates Open

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

OpenFreeEnergy/openfe#2102 · Opened Jul 27, 2026
Extensions: handling on-the-fly analyses Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

OpenFreeEnergy/openfe#2101 · Opened Jul 27, 2026
Extensions: Protocol updates Open

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

OpenFreeEnergy/openfe#2100 · Opened Jul 27, 2026
Extensions: multi-generation free energy analysis Open

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

OpenFreeEnergy/openfe#2099 · Opened Jul 27, 2026
Extensions: storing states / systems in relevant Protocols Open

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

OpenFreeEnergy/openfe#2098 · Opened Jul 27, 2026
Extensions: PlainMDProtocol Open

OpenFreeEnergy/openfe#2097 · 1 assignee · Opened Jul 27, 2026
Leftover items from continuations Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

OpenFreeEnergy/openfe#2096 · Opened Jul 27, 2026
Switch HybridTop multistate sampler creation to read in a list of of thermodynamic states Open

OpenFreeEnergy/openfe#2095 · 1 assignee · Opened Jul 27, 2026
Epic: ResultsNetwork Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

OpenFreeEnergy/openfe#2087 · Opened Jul 15, 2026
migrate ResultsNetwork to gufe? Open

OpenFreeEnergy/openfe#2086 · 1 assignee · Opened Jul 15, 2026
audit codebase to see where ResultsNetwork should be used Open

OpenFreeEnergy/openfe#2085 · 1 assignee · Opened Jul 15, 2026
openfe gather rewrite: use ResultsNetwork Open

OpenFreeEnergy/openfe#2084 · 1 assignee · Opened Jul 15, 2026
ResultsNetwork: add interoperability with AlchemicalArchive and FEMap Open

OpenFreeEnergy/openfe#2083 · 1 assignee · Opened Jul 15, 2026
Results handling: rewrite openfe protocols meet spec defined in #2077 Open

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

OpenFreeEnergy/openfe#2082 · Opened Jul 15, 2026
ResultsNetwork: design data structure(s) and API to meet specifications in #2077 Open

OpenFreeEnergy/openfe#2081 · 1 assignee · Opened Jul 15, 2026
add a ResultsNetwork class Open

OpenFreeEnergy/openfe#2079 · 1 assignee · Opened Jul 15, 2026
add a cookbook for collecting results Open

OpenFreeEnergy/openfe#2078 · 1 assignee · Opened Jul 15, 2026
ResultsNetwork: define requirements and specifications Open

OpenFreeEnergy/openfe#2077 · 1 assignee · Opened Jul 15, 2026
exorcist user-facing docs Open

OpenFreeEnergy/openfe#2075 · 1 assignee · Opened Jul 14, 2026
openfe gather should support json.gz Open

OpenFreeEnergy/openfe#2074 · 1 comment · 1 assignee · Opened Jul 13, 2026
update exorcist to use new gufe storage (breaking change) Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

OpenFreeEnergy/openfe#2073 · Opened Jul 13, 2026
warehouse: add user-facing docs Open

OpenFreeEnergy/openfe#2071 · 1 assignee · Opened Jul 13, 2026

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