Fixed cell parameters, TINKER I am using TINKER package to calculate the external reorganization energy for pentacene crystal. But I have problems with that - I've generated .xyz file of 5 molecules with VESTA and I need to perform the calculation on those five molecules (image below) with periodic boundary conditions (PBC). 



How can I find the proper size of cell and keep it fixed for calculations? When I use keywords A-axis, B-axis, C-axis and alpha, beta, gamma and assign lattice vectors and angles to them after optimization or minimization for the charged system like that apparently cell gets broken and molecules are distorted out of box:
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.