  We present a thermodynamically robust coarse-grained model to simulate
folding of RNA in monovalent salt solutions. The model includes stacking,
hydrogen bond and electrostatic interactions as fundamental components in
describing the stability of RNA structures. The stacking interactions are
parametrized using a set of nucleotide-specific parameters, which were
calibrated against the thermodynamic measurements for single-base stacks and
base-pair stacks. All hydrogen bonds are assumed to have the same strength,
regardless of their context in the RNA structure. The ionic buffer is modeled
implicitly, using the concept of counterion condensation and the Debye-H\"uckel
theory. The three adjustable parameters in the model were determined by fitting
the experimental data for two RNA hairpins and a pseudoknot. A single set of
parameters provides good agreement with thermodynamic data for the three RNA
molecules over a wide range of temperatures and salt concentrations. In the
process of calibrating the model, we establish the extent of counterion
condensation onto the single-stranded RNA backbone. The reduced backbone charge
is independent of the ionic strength and is 60% of the RNA bare charge at 37
degrees Celsius. Our model can be used to predict the folding thermodynamics
for any RNA molecule in the presence of monovalent ions.
