Irfan Alibay

Hi @PabloNA97, Apologies for the slow response. Unfortunately adding custom restraints isn't something that is possible with the OpenFE RBFE Protocol, however it is something that we have been considering...

@mikemhenry when you say "espaloma tests" do you mean "espaloma-charge tests"? As far as I can remember, I don't think we ever added espaloma FF tests anywhere in openfe.

Relevant openmmtools issue for numpy 2.0: https://github.com/choderalab/openmmtools/issues/772 Edit: wrong issue sorry 🤦🏽

Hi @BillSwope, Thanks so much for this bug report! We have seen similar cases in the past. Under normal operations you shouldn't end up with duplicate entries in `to_del`, although...

From @BillSwope (via slack): Kartograf was used for the mapper. Here is how the network was constructed for the case that failed. ``` mapping_filters = [ filter_ringbreak_changes, # default filter_ringsize_changes,...

Moving tracking the error message fix to #1093 but otherwise we can consider this as "solved".

> I think what @IAlibay means is that there is a nested exception error message: > > which is kinda ugly. you can explicitly suppress the chaining of exceptions using...

@lilyminium can you point out to which specific sub-issue you're fixing under https://github.com/MDAnalysis/mdanalysis/issues/4748?

Can you please add in the test from #4750 if it's fixing it too?

> found it confusing that AnalysisBase added times and frames to results. @orbeckst from my understanding it's the other way around? AnalysisBase doesn't have times and frames is results but...