OpenFreeEnergy/pontibus

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Experimental OpenFE Protocols for Force Field Evaluation

Stars: 5
Forks: 3
Open beginner issues: 0
Indexed issues: 49
Avg merge: 2d 23h
Merged PRs (30d): 4

Dominant language: Python
License: MIT
Last GitHub push: Sep 9, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

49 open issues indexed

Sigma=epsilon=0 for virtual sites Open

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

OpenFreeEnergy/pontibus#210 · Opened Sep 1, 2026
RTD build is failing Open

OpenFreeEnergy/pontibus#207 · 1 comment · 1 assignee · Opened Aug 29, 2026
Use `openff-packmol` instead of interchange for packmol interface imports Open

OpenFreeEnergy/pontibus#205 · 1 assignee · Opened Aug 29, 2026
Water Component isn't Named Open

OpenFreeEnergy/pontibus#187 · 3 comments · 1 assignee · Opened Mar 6, 2026
Deduplicate InterchangeOpenMMSolvationSettings Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

OpenFreeEnergy/pontibus#155 · 1 comment · Opened Oct 8, 2025
Clean up system creation tests Open

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

OpenFreeEnergy/pontibus#150 · Opened Oct 3, 2025
InterchangeOpenMMSolvationSettings is misleading since PackmolSolvationSettings also goes through Interchange Open

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

OpenFreeEnergy/pontibus#149 · Opened Oct 3, 2025
Review need for SLTCAP ion addition in OpenMM Solvation Open

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

OpenFreeEnergy/pontibus#148 · Opened Oct 3, 2025
Test parameter assignment of different components Open

Difficulty 3/5 1-2 days Newbie friendliness 50/100

OpenFreeEnergy/pontibus#144 · Opened Sep 17, 2025
CI tests are too long Open

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

OpenFreeEnergy/pontibus#142 · Opened Sep 15, 2025
Have a library charge check for protein parsing Open

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

OpenFreeEnergy/pontibus#129 · Opened Aug 12, 2025
RFE Protocol: structural analysis is not working Open

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

OpenFreeEnergy/pontibus#117 · Opened Jul 28, 2025
Add integration tests that check equilibration (ASFEProtocol) Open

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

OpenFreeEnergy/pontibus#116 · Opened Jul 24, 2025
Add HybridTop user documentation Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

OpenFreeEnergy/pontibus#106 · Opened Jul 20, 2025
Add HybridTop usage notebook Open

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

OpenFreeEnergy/pontibus#105 · Opened Jul 20, 2025
Alchemiscale Deployment Open

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

OpenFreeEnergy/pontibus#103 · Opened Jul 20, 2025
Conda-forge release Open

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

OpenFreeEnergy/pontibus#102 · Opened Jul 20, 2025
Release v0.1 Open

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

OpenFreeEnergy/pontibus#101 · Opened Jul 20, 2025
Update system creation tooling for virtual site support Open

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

OpenFreeEnergy/pontibus#95 · Opened Jul 20, 2025
Add virtual site support to HTF subclass Open

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

OpenFreeEnergy/pontibus#92 · Opened Jul 20, 2025
Add ExtendedSolventComponent support to HybridTopologyProtocolUnit Open

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

OpenFreeEnergy/pontibus#88 · Opened Jul 20, 2025
HybridTop Protocol Deployment and Documentation Open

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

OpenFreeEnergy/pontibus#76 · Opened Jul 20, 2025
Virtual site support: user stories Open

OpenFreeEnergy/pontibus#65 · 3 comments · 2 assignees · Opened Jun 17, 2025
SFEs: Experimental virtual site support Open

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

OpenFreeEnergy/pontibus#64 · Opened Jun 17, 2025
Assigning partial charges ahead of time may not work for virtual sites Open

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

OpenFreeEnergy/pontibus#60 · 1 reaction · Opened May 26, 2025
Validate for OpenMM 8.2 Open

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

OpenFreeEnergy/pontibus#56 · Opened May 22, 2025
Benchmark systems list Open

OpenFreeEnergy/pontibus#52 · 4 comments · 1 reaction · 1 assignee · Opened Mar 10, 2025
Add user guide documentation Open

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

OpenFreeEnergy/pontibus#50 · Opened Feb 12, 2025
Add tests for passing box vectors Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

OpenFreeEnergy/pontibus#49 · 1 comment · Opened Feb 12, 2025
Add warning & test for non-ExtendedSolventComponent conformer generation Open

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

OpenFreeEnergy/pontibus#48 · Opened Feb 10, 2025
Verify the extended solvent component retains conformer & partial charge properties on serialization roundtrip Open

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

OpenFreeEnergy/pontibus#47 · Opened Feb 10, 2025
Alchemical virtual site Experimental factory tests Open

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

OpenFreeEnergy/pontibus#45 · Opened Feb 10, 2025
Add alchemical species with virtual sites Protocol tests Open

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

OpenFreeEnergy/pontibus#44 · Opened Feb 10, 2025
Add test for extended solvent component but an offmol input without conformer Open

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

OpenFreeEnergy/pontibus#43 · Opened Feb 10, 2025
Add experimental factory validation tests Open

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

OpenFreeEnergy/pontibus#41 · Opened Feb 10, 2025
Add Protocol tests for experimental factory. Open

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

OpenFreeEnergy/pontibus#40 · Opened Feb 10, 2025
Review appropriateness of `collate=True` when creating openmm topologies with virtual sites. Open

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

OpenFreeEnergy/pontibus#34 · Opened Feb 3, 2025
Add explicit non-solvent dry run test Open

OpenFreeEnergy/pontibus#28 · 1 comment · 1 assignee · Opened Jan 27, 2025
Gather utility Open

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

OpenFreeEnergy/pontibus#19 · Opened Sep 24, 2024
Cookbook [Python API execution and gathering] Open

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

OpenFreeEnergy/pontibus#18 · Opened Sep 24, 2024
Cookbook [CLI execution] Open

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

OpenFreeEnergy/pontibus#17 · Opened Sep 23, 2024
Add user tutorial [non-water solvent] Open

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

OpenFreeEnergy/pontibus#16 · Opened Sep 23, 2024
Add user tutorial [water solvent] Open

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

OpenFreeEnergy/pontibus#15 · Opened Sep 23, 2024
Add full simulation integration tests [solvent] Open

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

OpenFreeEnergy/pontibus#12 · Opened Sep 23, 2024
Add full simulation integration tests [vacuum] Open

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

OpenFreeEnergy/pontibus#11 · Opened Sep 23, 2024
Add charge backend tests Open

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

OpenFreeEnergy/pontibus#10 · Opened Sep 23, 2024
Add non-cubic box tests Open

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

OpenFreeEnergy/pontibus#9 · Opened Sep 23, 2024
Add virtual site solvent alchemical system tests Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

OpenFreeEnergy/pontibus#8 · Opened Sep 23, 2024
Add user charge tests Open

OpenFreeEnergy/pontibus#7 · 1 assignee · Opened Sep 23, 2024

OpenFreeEnergy/pontibus

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