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What is the common aspect of these two molecules that you want to simulate?
There are many different types of computational models that span from the simple and computationally cheap "molecular mechanics" to slightly better semi-empirical methods like "extended Hückel" to the very expensive, but much more accurate "Density Functional Theory", which can give excellent analysis and prediction of molecules and molecular interactions, including electronic structure, orbital coupling and charge or spin density localization.As far as software goes, Gaussian is the one that I have used most, and is often used in academic settings, but it is really freaking expensive. It is capable of all the methods I mentioned above and more--it's really one for the pros. Another fairly expensive program is VASP, which might be better suited to modeling graphene and other 2D or 3D lattices.There is a freeware program called Avogadro that will do some simple molecular mechanics modeling (UFF = universal force field), but it is annoying to work in, and I don't know how informative the outputs will be for your DNA/graphene system...Another freeware program, YAeHMOP (available at sourceforge), does extended Hückel calculations, and is actually quite powerful, though the interface is not great...Good luck!
graphene helps determine the sequence of nucleobases in DNA
Quote from: dveansgraphene helps determine the sequence of nucleobases in DNA Are you developing a next-generation DNA sequencing technology?Or are you trying to discover the evolutionary tree of DNA? (This is covered in another thread...)