Universe doesn't fill to the number density very well

**Description of the error**
```python
from MDMC.MD import Atom, Universe

density = 0.0176
universe = Universe(dimensions=38.4441)
Ar = Atom('Ar[36]', charge=0.)
universe.fill(Ar, num_density=density)
print(f"density {universe.density}")

density = 0.0176
universe = Universe(dimensions=45.0)
Ar = Atom('Ar[36]', charge=0.)
universe.fill(Ar, num_density=density)
print(f"density {universe.density}")
```

The density is very different despite requesting the same num_density.

**Describe the expected result**
Should have a similar density.

**Describe the actual result**
```
Universe created with:
Dimensions [38.44 38.44 38.44]
density 0.6330262453786744 amu / Ang ^ 3
Universe created with:
Dimensions [45. 45. 45.]
density 0.5253531313984148 amu / Ang ^ 3
```