I am glad you were able to realize the large deformations! Introducing granules will not be an easy accomplishment. If I understand the situation, modeling their interaction with contact in Mechanical will be time-consuming, not to mention that each granule will want to have 6 DOFs, so this simulation will typically need to be run in a transient dynamic. There are ways to solve with Mechanical, but other methods too using LS Dyna or combining Rocky DEM to model the interactions of the granules with the mechanical, but let's take a step back to try and simplify...
The negative pressure is the vacuum. You apply that negative pressure. If the space can not completely close because of granules, then we can introduce offsets in the frictionless/frictional contacts that would act to prevent the space from completely collapsing. Have a look at the offset in the contact details. If you enter a positive offset, then the contact will take place that offset off of the surface. This can possibly be used as a rough way to have a stop/jam as the contacts start to interact. You would have to do some trial and error in the offsets, and which faces can touch which faces, but see if this is something you can try to incorporate.