  Coarse-grained models can be of great help to address the problem of
structure prediction in nucleic acids. On one hand they can make the prediction
more efficient, while on the other hand, they can also help to identify the
essential degrees of freedom and interactions for the description of a number
of structures. With the aim to provide an all-atom representation in an
explicit solvent to the predictions of our SPlit and conQueR (SPQR)
coarse-grained model of RNA, we recently introduced a backmapping procedure
which enforces the predicted structure into an atomistic one by means of
steered Molecular Dynamics. These simulations minimize the ERMSD, a particular
metric which deals exclusively with the relative arrangement of nucleobases,
between the atomistic representation and the target structure. In this paper,
we explore the effects of this approach on the resulting interaction networks
and backbone conformations by applying it on a set of fragments using as a
target their native structure. We find that the geometry of the target
structures can be reliably recovered, with limitations in the regions with
unpaired bases such as bulges. In addition, we observe that the folding pathway
can also change depending on the parameters used in the definition of the ERMSD
and the use of other metrics such as the RMSD.
