Simulation of DNA is carried out by computation programmen , in this manner the process reached to high time consumed rate of calculations with ultra computer processor. therefore fragmentation of DNA is a good way to reduced these challenge .
You cannot calculate structural properties of DNA by simulation of a few purine bases.DNA consists of bases i.e purines and pyrimidines plus a deoxyriboses(sugar) - phosphate backbone which connects the bases via phosphodiester bonds.In addition DNA swims in salty water and its parts interact strongly with each other and this microenvironment.As Aristoteles said the whole is much bigger than the sum of its parts and I think the problem you address is more brutal than the biggest computer brutes available.However some insights have been gained via decades of experimental work and clever theoretical approximations and computations.I am afraid you will have first to study all this background material before contributing something relevant.