Calculating the spectroscopic properties of complex conjugated organic molecules in their relaxed state is far from simple. An additional complexity arises for flexible molecules in solution, where the rotational energy barriers are low enough so that non-minimum conformations may become dynamically populated. These metastable conformations quickly relax during the minimization procedures preliminary to DFT calculations, and so accounting for their contribution to the experimentally-observed properties is problematic. We describe a strategy for stabilising these non-minimum conformations in silico, allowing their properties to be calculated. Diadinoxanthin and alloxanthin present atypical vibrational properties in solution, indicating the presence of several conformations. Performing energy calculations in vacuo and polarizable continuum model calculations in different solvents, we found three different conformations with values for the δ dihedral angle of the end-ring ca. 0°, 180° and 90° with respect to the plane of the conjugated chain. The latter conformation, a non-global minimum, is not stable during the minimization necessary for modelling its spectroscopic properties. To circumvent this classical problem we used a Car-Parinello MD supermolecular approach, in which diadinoxanthin was solvated by water molecules so that metastable conformations were stabilized by hydrogen bonding interactions. We progressively removed the number of solvating waters to find the minimum required for this stabilisation. This strategy represents the first modelling of a carotenoid in a distorted conformation, and provides an accurate interpretation of the experimental data.