Irfan Alibay

This is low priority, but it would be amazing if we could get it merged sooner than later.

> This looks good to me! Just out of curiosity (might be a dumb question): how would you specify the density of molecules in the box? I don't think it's...

> > This looks good to me! Just out of curiosity (might be a dumb question): how would you specify the density of molecules in the box? > > I...

@hannahbaumann if you have time could you have another look at this? I'd like to get to a point where we can merge this but I definitely want your stamp...

> This could use a changelog entry, otherwise it is good to go! Good call, done!

Initial thought here is that OpenMM modeller is adding hydrogens based on the OpenMMFF templates. Probably would want to check that there are missing hydrogens and throw an error at...

@davidlmobley thanks for opening up this issue. This is a bit of an obscure part of the HTF, so it might take us a little bit to come up with...

@davidlmobley this is a particularly complicated topic, apologies for the rather lengthy response. The OpenFE team did quite the deep dive on this (particularly thanks to @hannahbaumann). Happy to go...

Thanks @zhang-ivy and @sukritsingh I need to review the above papers (so apologies if the answer is already there). One immediate thought here is whether or not a > 1...

Thanks for raising this issue @jingqiong, PR #752 has been opened to try to address this.