openfe-failure-cases

This repository collects OpenFE simulation failure cases so we can better understand what fails, why it fails, and under what conditions. The goal is to support protocol improvements by sharing reproducible examples, diagnostics, and context around crashes, NaN results, and large repeat-to-repeat variation.

What counts as a failure

In this repository, "failure" means a simulation that:

• crashes
• returns NaN
• shows large variation between repeats, typically around ~5 kcal/mol or more

This does not mean a result is scientifically incorrect just because it differs from a reference value.

Submission

To make a submission, please fork this repository and create a pull request with your case(s), and fill in the submission template. Multiple cases can be submitted in a single pull request, but please submit each case in its own folder containing the transformation JSON, logs and any other output files.

What to include

Please submit cases with as much context as possible, including:

• the OpenFE transformation JSON
• environment details
• hardware details
• any diagnostics already run
• For NaNa failures the xml file of the last state before the crash, stored in nan_error_logs

Example submission

You can find an example of a failure case submission here: #2