This is an implementation of the "two-stage" model used by Maxim Imakaev
in the Naumova et Al 2013 Science paper on metaphase chromatin.
(Download the supplemental materials section and scroll down to the section:
 "Two-stage process: linear compaction - axial compression")

---- SMALL MODIFICATION ----

Unlike that study, I did not use "softened" Lennard-Jones potentials
(which allow the chains to pass through each other).

--- Why use moltemplate? ---

Honestly, you don't need to use moltemplate to build this polymer.
It is almost counter-productive to use moltemplate to build this kind of
polymer because it is so simple.  (The polymer has only 1 bead per atom.
It just makes it more complicated to introduce all these extra 
files including monomer.lt, condensin.lt and system.lt, especially considering
that system.lt is a complex file which is generated by a separate script.)

However building the sytem using moltemplate may pay off if you
replace each point-like monomer with a multi-atom molecule later on.
(Right now, using moltemplate to build this system is sort of overkill.
 I'll post an example of building more complex models of chromatin eventually.)

---- 30-nm fiber model: ----

Anyway, the two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section.

For the 10nm model, 
    n=128000, 
    L=200, 
    U(alpha)=5*(1 - cos(alpha))
    bond_length=1.0     (=10nm)
    sigma=1.0 (particle radius = 10nm)

30nm-fiber model details:
"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level."

I interpret this to mean that, for the 30nm model, 
    n=128000/4.25~=30117   (however I rounded up to 32768=2^15)
    L=200/4.25~=47         (however I rounded up to 51)
    U(alpha)=1.17647*(1 - cos(alpha))    (5/4.25=1.17647)

To increase the volume by a factor o 4.25, I increase both the diameter of each
bead (the "sigma" parameter), and the bond-lengths connecting them from 
1.0 (corresponding to 10nm) to 4.25^(1/3)~=1.6198 (corresponding to 16.198nm).