Zach Kagin

@mattwthompson @sukritsingh Would one of you be able to review this small PR? Thank you!

Yes, my apologies - it's the atom serial number. I believe this happens (in our case) when a ligand is added to an already solvated system, leading to more than...

Unfortunately I don't have the bandwidth to continue pursuing this fix into master. We've patched it in an internal fork and it works correctly for us, and the Hex workaround...

What is the expected behavior of rigidWaters=True in regards to true rigidity? Using the AMBER forcefield and tip3p water model, what we see is: - With no changes, waters change...

Attached are input XML/prmtop files of a solvated + equilibrated 4W53 system and the result DCD file, along with some demo code that mirrors what we're doing as closely as...

From what I understand, the cause of the unusual prmtop is that the system is prepared initially with OpenMM rigidWater=False. That is done because it is later read in/out of...

Yep. Just to confirm, the end result we want is an ever-growing list of deleted StudentSubmissions, correct? And built so that we can use this logic for any of the...

Yep, the cleanest way is probably a soft delete pattern, where there's an additional "deleted" column. The downside is then we start needing to deal with schema migrations, since we...

@dchess Just checking in on this again — let me know if you like the described approach or if you had something else in mind.

Yep, if you don't need to know which student submissions are from deleted / removed students, then we shouldn't need a delete column. That might be a short-term answer to...