what's this new feature supposed to do?
What's the packing fraction of your system, do you use NPT?
The final packing fraction in amorphous systems, or glass transition temperature is dependent on your cooling rate and it should scale linearly with it..
Hence the longer you simulate the larger packing fraction (lower free volume fraction) you obtain. Scaling with temperature, i.e. how much volume changes with given change of cooling rate is given by fragility index.
Fragility should be related to softness, or how much your beads overlap..