Yes, I agree. Cell lists are a key missing feature in Molly.jl. I am moving to a position this autumn which will let me focus on Molly full time, hopefully it will progress quickly after that and become useful for serious work. The topology tools are barebones at the minute but I’m hoping to depend on Chemfiles for that.
I can see a nice molecular simulation ecosystem starting to emerge over the next few years. I am excited for a Julia version of Packmol, that could become a crucial package.