I am gonna make a guess because I’ve seen this system many times: Most likely you are placing CNTs within a very viscous polymer at ambient temperature and pressure. Given the viscosity of the system, it would take a very long time to reach the state where all the vacuum pockets were removed. A solution could be to pre-equilibrate the system using larger pressure or temperature.
This is a simulation of dispersing CNTs in a DMAc solution. It was not easy to create a model with CNTs dissolved in solution from the beginning, so we put three CNTs in the center and put the solvent model on top and bottom. Afterwards, we wanted to see the behavior of CNTs in solvent through NPT equlibration. However, the size of the box could not be reduced to fit the solvent model.