  Although RNAs play many cellular functions little is known about the dynamics
and thermodynamics of these molecules. In principle, all-atom molecular
dynamics simulations can investigate these issues, but with current computer
facilities, these simulations have been limited to small RNAs and to short
times.
  HiRe-RNA, a recently proposed high-resolution coarse-grained for RNA that
captures many geometric details such as base pairing and stacking, is able to
fold RNA molecules to near-native structures in a short computational time. So
far it had been applied to simple hairpins, and here we present its application
to duplexes of a couple dozen nucleotides and show how with our model and with
Replica Exchange Molecular Dynamics (REMD) we can easily predict the correct
double helix from a completely random configuration and study the dissociation
curve. To show the versatility of our model, we present an application to a
double stranded DNA molecule as well.
  A reconstruction algorithm allows us to obtain full atom structures from the
coarse-grained model. Through atomistic Molecular Dynamics (MD) we can compare
the dynamics starting from a representative structure of a low temperature
replica or from the experimental structure, and show how the two are
statistically identical, highlighting the validity of a coarse-grained approach
for structured RNAs and DNAs.
