anna

Thank you for all the suggestions! They're really helpful :smile: Initially I wasn't sure with regards to implementing it on a protocol level as that could lead to multiple HMR...

> For information for the near future, I have been adding more capability to the search syntax as part of the modernisation of the Sire API. This makes the searching...

That makes sense, thank you!

Thank you so much for all the feedback 😊 I'm also currently doing some large scale analysis to check the reproducibility between the statistical inefficiency / autoequilibration detection and other...

Another potential further thing for analysis, that is implemented for now very roughly in the workshop for the sake of the absolute analysis (6aaae504d04d1d3bdef0b3bdf69caccf6ace2017 , fixed in d084e58658878811f48c77cda22f5dcba00da6e8, warnings in...

> Another potential further thing for analysis, that is implemented for now very roughly in the workshop for the sake of the absolute analysis ([6aaae50](https://github.com/michellab/BioSimSpace/commit/6aaae504d04d1d3bdef0b3bdf69caccf6ace2017) , fixed in [d084e58](https://github.com/michellab/BioSimSpace/commit/d084e58658878811f48c77cda22f5dcba00da6e8), warnings...

Just to add on to this, pymbar is a dependency for alchemlyb, as alchemlyb does end up feeding the extracted data into pymbar during the MBAR analysis. This is also...

Hello! Sorry for taking so long to reply, I've also been having issues with SOMD crashing w all runs (2 and 4 fs) and am still trying to figure those...

I think it is to a certain extent - if I use the recently generated input files with the 2021 sire, the crash is related to the input files having...

> For the first exception you list, is this just from downgrading Sire, or BioSimSpace too? It seems related to [this](https://github.com/michellab/BioSimSpace/issues/275) issue, which was added in the 2022.1.0 release of...