Molecular Dynamics Software and DNA

A quick overview:

http://en.wikipedia.org/wiki/DNA_nanotechnology

From here, a list of useful resources are provide....e.g. Erik Winfree group at Caltech is one

However, I'm not so sure if it is possible for one to read these stuffs and just pick it up

Mfold
Dnamelt
etc.... the problem is I don't know how to read or interpret the results

And then softwares:

Ascalaph  (extremely pretty-looking)
cadNano (strictly DNA origami)
nano-engineer