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| This guide covers tips and strategies for troubleshooting simulation failures. | ||
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Should we add something to say if you have a unique failure case not explained by the points here consider uploading it the the failure repo or making an issue?
IAlibay
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IAlibay
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Could you also fill in the LLM declaration please?
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| **Suggested fixes** | ||
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| - Run ``scripts/validate_transformation.py`` on the transformation JSON to try to identify the source of the problem. |
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This script isn't in openfe - where should they be accessing it?
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Good catch, now linking to it.
| https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan | ||
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| These errors usually mean that the simulation became numerically unstable during minimization or propagation. | ||
| In some cases the simulation can be rescued by restarting from the last stable state, by default the protocols will attempt this up to ``20`` times before giving up and so you may see multiple ``NaN`` errors in the logs. |
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Something here is missing about what to do if they see the logs but the simulation is still running - should they trust their results, etc....
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Hmm good point, I guess we should advise them to check the transformation and try to identify what might be causing the stability issues before trusting the results, and also check other things like the deviation between repeats to assess its trustworthiness? Basically general caution if they have to be restarted many times?
| Explanations of key concept underlying the OpenFE toolkit. | ||
| Explanations of key concepts underlying **openfe**. | ||
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| .. grid-item-card:: :fas:`life-ring` Troubleshooting |
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I would like to hear from @atravitz here, but to me having 7 items on this grid pattern significantly worsens the user experience. Either we drop another card, add more cards, or just don't include this.
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Yeah I just wasn't sure where to put it to make it noticable the cards draw the eye on that page and I didn't want it getting lost as its an important addition, happy to change though!
| :link-type: doc | ||
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| Step-by-step examples showing how to use the OpenFE toolkit. | ||
| Step-by-step examples showing how to use the **openfe**. |
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I think the original intent here was to use "OpenFE" because it wasn't just openfe the package, but tutorials showing how to use the whole ecosystem.
It's a small distinction, but maybe one worth keeping.
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Ah okay, it just didn't seem consistent with the rest of that page and maybe we should just say "tools from the OpenFE ecosystem"? or make it clear that the "OpenFE toolkit" refers to this?
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
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Description
Begin moving the troubleshooting guide developed on the failure cases repo to openfe main docs.
Fixes #1757
LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no
If yes, please provide details here: Yes used to format the section and fix the rst style headings on the troubleshooting page.
Checklist
newsentry, or the changes are not user-facing.pre-commit.ci autofix.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
Developers certificate of origin