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OpenFreeEnergy

18 indexed repositories · View on GitHub

openfe
The Open Free Energy toolkit

Python · 331 stars
ExampleNotebooks
Notebooks demonstrating how to do simple tasks related to free energy calculations.

Jupyter Notebook · 70 stars
IndustryBenchmarks2024
Repository for the 2024 OpenFE industry benchmark efforts

Jupyter Notebook · 48 stars
Lomap
Alchemical mutation scoring map

Python · 45 stars
gufe
core data models of the Open Free Energy ecosystem

Python · 45 stars
cinnabar
Package for consistent reporting of relative free energy results

Python · 43 stars
kartograf
This package contains tools for setting up hybrid-topology FE calculations

Python · 39 stars
alchemiscale
a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home

Python · 36 stars
konnektor
Algorithms for various Network Layouts and Tooling for planning FE Calculations

Jupyter Notebook · 24 stars
feflow
Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits

Python · 20 stars
openfe_analysis
Structural analysis tools for OpenFE free energy calculations, built on MDAnalysis.

Python · 20 stars
openfe-benchmarks

Python · 13 stars
openfe-failure-cases
A collection of reproducible openfe protocol failure cases resulting in NaN results.

Python · 5 stars
pontibus
Experimental OpenFE Protocols for Force Field Evaluation

Python · 5 stars
alchemiscale-fah
protocols and compute service for using alchemiscale with Folding@Home

Python · 3 stars
openfreeenergy.github.io

HTML · 2 stars
exorcist
Daemonless campaign-scale simulation orchestration

Python · 2 stars
alchemiscale.org-deployment
deployment versioning and artifact generation for alchemiscale.org alchemiscale instances

HCL · 0 stars

Beginner friendly Everything

Open All

Add docs for accessing protocol results Open

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

OpenFreeEnergy/openfe#2198 · Opened Sep 18, 2026
Update docs for Concatenator updates Open

OpenFreeEnergy/konnektor#276 · 1 reaction · 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 · Opened Sep 17, 2026
rename fixture names for clarity Open

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

OpenFreeEnergy/gufe#836 · Opened Sep 17, 2026
rename orchestration fixture names for clarity Open

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

OpenFreeEnergy/openfe#2195 · 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 · 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 · Opened Sep 16, 2026
Structural analysis for ABFEs Open

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

OpenFreeEnergy/openfe#2191 · 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 · 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
`ProteinMembraneComponent` serialization/deserialization is incredibly slow Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

OpenFreeEnergy/gufe#835 · 1 comment · Opened Sep 8, 2026
Cycle closure dataframe hangs on large networks Open

OpenFreeEnergy/cinnabar#238 · 1 assignee · Opened Sep 8, 2026
Implement a `RedundantMSTConcatenator` Open

OpenFreeEnergy/konnektor#272 · 1 assignee · Opened Sep 7, 2026
Provenance for Concatenators Open

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

OpenFreeEnergy/konnektor#271 · Opened Sep 7, 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
CLD Labels change depending on the sources provided Open

OpenFreeEnergy/cinnabar#237 · 1 assignee · Opened Sep 4, 2026
Unexpected large excluded atoms from mappings Open

OpenFreeEnergy/kartograf#166 · 3 assignees · Opened Sep 2, 2026
Document issues with process limits Open

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

OpenFreeEnergy/openfe#2179 · Opened Sep 1, 2026
Sigma=epsilon=0 for virtual sites Open

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

OpenFreeEnergy/pontibus#210 · Opened Sep 1, 2026
Add `.offxml` to small molecule force field settings entry. Open

OpenFreeEnergy/gufe#833 · 1 assignee · 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
Validation ideas Open

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

OpenFreeEnergy/openfe-failure-cases#8 · 1 comment · 1 reaction · Opened Aug 27, 2026
Make all plotting functions return subplots Open

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

OpenFreeEnergy/cinnabar#235 · Opened Aug 21, 2026
Should `SmallMoleculeComponent` pull charges from a mol2 input Open

Difficulty 4/5 3-5 days Newbie friendliness 50/100

OpenFreeEnergy/gufe#828 · Opened Aug 21, 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 · 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
Option for Concatenators to exclude certain edges Open

OpenFreeEnergy/konnektor#266 · 1 reaction · 1 assignee · Opened Aug 19, 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 · Opened Aug 18, 2026
`merge_networks` does not update reference network during iteration Open

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

OpenFreeEnergy/konnektor#265 · Opened Aug 14, 2026
Update documentation to reflect package rather than integration Open

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

OpenFreeEnergy/exorcist#51 · Opened Aug 12, 2026
Update sphinx theme to match with the rest of OpenFE Open

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

OpenFreeEnergy/exorcist#50 · Opened Aug 12, 2026
Refactor task_type from 1-1 to 1-many Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

OpenFreeEnergy/exorcist#49 · Opened Aug 11, 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

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