May be this is what you want:
h = 10;
l = 6;
w = 4;
r = 0.2;
atoms = Table[
Sphere[{RandomReal[w - r], RandomReal[l - r], RandomReal[h - r]},
r], 240];
Manipulate[
Graphics3D[{Opacity[0.2],
Parallelepiped[{0, 0, 0}, {{w, 0, 0}, {0, l, 0}, {0, 0, h}}],
Opacity[0.5], Red, atoms[[1 ;; n]]}, Axes -> True,
AxesStyle -> GrayLevel[0], ViewPoint -> {1.3, -2.4, 2.}], {n, 0,
240, 1}]