Fixed cell parameters, TINKER
It's a little hard to tell from your second visualization, but to me, it simply seems as if the molecules have shifted somewhat with respect to the periodic box.

A unit cell or periodic boundary "box" is simply a frame of reference. There's no walls. The molecules don't "see" it. 

It's merely an indication that there's translational symmetry. In short, in the left-hand view of the second image, the molecule "breaking the box" is also wrapped around into the box by translational symmetry.

I don't know what visualization tool you're using, but if you display more than one unit cell, you'll easily see that the molecules "wrap" around.