Create a hole inside a box

Hello all,


I have two immiscible liquid in my simulation box. I want to create a sphere hole in the middle of the box, remove any atom and molecules and fill the hole with a nanoparticle. I need to perform a dynamic run before adding the nanoparticle, so the option of putting nanoparticle before the box construction is impossible. 

Any suggestion is appreciated.


Thanks,

Abolfazl