OpenFreeEnergy/ExampleNotebooks

View on GitHub

Notebooks demonstrating how to do simple tasks related to free energy calculations.

Stars: 70
Forks: 15
Open beginner issues: 0
Indexed issues: 38
Avg merge: 10h 42m
Merged PRs (30d): 2

Dominant language: Jupyter Notebook
License: MIT
Last GitHub push: Sep 15, 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

38 open issues indexed

Merge cinnabar-absolute and cinnabar RBFE plotting docs Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

OpenFreeEnergy/ExampleNotebooks#313 · Opened Jun 15, 2026
add headers to notebooks Open

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

OpenFreeEnergy/ExampleNotebooks#292 · Opened Feb 11, 2026
do we still want a colab link on PRs now what we have ReviewNB? Open

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

OpenFreeEnergy/ExampleNotebooks#279 · 1 comment · Opened Dec 11, 2025
fix all warnings shown in example notebooks Open

OpenFreeEnergy/ExampleNotebooks#277 · 1 comment · 1 assignee · Opened Dec 10, 2025
pin google colab runtime Open

OpenFreeEnergy/ExampleNotebooks#241 · 1 reaction · 1 assignee · Opened Oct 21, 2025
add a `How to change water model notebook` Open

OpenFreeEnergy/ExampleNotebooks#189 · 1 assignee · Opened Feb 11, 2025
add solvation details to showcase notebook Open

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

OpenFreeEnergy/ExampleNotebooks#183 · Opened Dec 4, 2024
User Guide review: execution Open

OpenFreeEnergy/ExampleNotebooks#178 · 1 assignee · Opened Nov 7, 2024
should we still reference Perses in showcase notebook? Open

documentation

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

OpenFreeEnergy/ExampleNotebooks#165 · 1 comment · Opened Oct 9, 2024
To commit or not commit notebook output... Open

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

OpenFreeEnergy/ExampleNotebooks#164 · 4 comments · Opened Oct 9, 2024
Add examples to use multiple GPUs on HPC Open

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

OpenFreeEnergy/ExampleNotebooks#159 · 1 comment · Opened Sep 9, 2024
Remove `benchmark_demo` notebook? Open

Difficulty 1/5 Under an hour Newbie friendliness 48/100

OpenFreeEnergy/ExampleNotebooks#154 · Opened Jul 23, 2024
Run OpenFE Doc building in this repo Open

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

OpenFreeEnergy/ExampleNotebooks#142 · Opened May 7, 2024
TKY2 Result failure with gather Open

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

OpenFreeEnergy/ExampleNotebooks#141 · Opened May 2, 2024
Slim down results pulled into showcase Open

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

OpenFreeEnergy/ExampleNotebooks#140 · Opened May 1, 2024
Test everything that can be tested Open

OpenFreeEnergy/ExampleNotebooks#130 · 1 comment · 1 assignee · Opened Apr 21, 2024
Showcase: Cinnabar usage Open

OpenFreeEnergy/ExampleNotebooks#114 · 1 assignee · Opened Mar 4, 2024
Showcase: Include structural analysis section Open

OpenFreeEnergy/ExampleNotebooks#113 · 1 assignee · Opened Mar 4, 2024
Showcase: Include energetics analysis section Open

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

OpenFreeEnergy/ExampleNotebooks#112 · Opened Mar 4, 2024
Showcase: Include data created by execution in notebook repo Open

OpenFreeEnergy/ExampleNotebooks#111 · 1 assignee · Opened Mar 4, 2024
Showcase: Document atom mapping scoring metrics Open

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

OpenFreeEnergy/ExampleNotebooks#107 · 1 comment · Opened Mar 4, 2024
Notebook for RHFEs Open

1.0docdrive enhancement

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

OpenFreeEnergy/ExampleNotebooks#93 · Opened Jan 19, 2024
Make cookbook materials fetchables Open

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

OpenFreeEnergy/ExampleNotebooks#87 · Opened Oct 10, 2023
py3Dmol widgets not working Open

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

OpenFreeEnergy/ExampleNotebooks#82 · 1 comment · Opened Sep 1, 2023
Add Coverage Reports Open

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

OpenFreeEnergy/ExampleNotebooks#80 · Opened Aug 22, 2023
reference data for TYK2 example Open

1.0docdrive

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

OpenFreeEnergy/ExampleNotebooks#76 · 1 comment · Opened Jul 13, 2023
Mention of OpenFF biopolymer FF is misleading Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

OpenFreeEnergy/ExampleNotebooks#74 · Opened Jun 28, 2023
Dry run does not return an empty dictionary Open

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

OpenFreeEnergy/ExampleNotebooks#54 · Opened Apr 28, 2023
Test easyCampaign Open

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

OpenFreeEnergy/ExampleNotebooks#51 · 4 comments · Opened Apr 19, 2023
Add README files to all data clarifying provenance and status Open

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

OpenFreeEnergy/ExampleNotebooks#49 · Opened Apr 12, 2023
Update READMEs Open

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

OpenFreeEnergy/ExampleNotebooks#48 · Opened Apr 12, 2023
Rename openmm-rbfe to just relative_free_energy Open

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

OpenFreeEnergy/ExampleNotebooks#47 · Opened Apr 12, 2023
setup unclear for a data repository Open

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

OpenFreeEnergy/ExampleNotebooks#45 · Opened Apr 12, 2023
Clean up casing for notebooks Open

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

OpenFreeEnergy/ExampleNotebooks#43 · Opened Apr 12, 2023
update wget command Open

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

OpenFreeEnergy/ExampleNotebooks#34 · Opened Jan 19, 2023
remove fetch command Open

1.0docdrive

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

OpenFreeEnergy/ExampleNotebooks#21 · 1 comment · Opened Aug 5, 2022
Installation instructions Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

OpenFreeEnergy/ExampleNotebooks#12 · Opened Apr 7, 2022
Update License Open

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

OpenFreeEnergy/ExampleNotebooks#4 · Opened Mar 1, 2022

OpenFreeEnergy/ExampleNotebooks

Get new issues in your inbox