RNA plays a central role in many biological processes and is therefore an important target for drug development. In recent years an increasing wealth of structural and functional information about RNA-ligand complexes has been obtained using in vitro selected RNAs (aptamers). However, all those studies focused on structure and changes of the nucleic acid and mostly considered the ligand as a rigid target. Experimental characterization of the dynamics of a malachite green (MAG)-RNA aptamer complex revealed surprisingly asymmetric changes in the C-13 chemical shift of the ligand methyl groups, which indicate that the dye undergoes changes in its conformation and charge distribution upon binding, in addition to the red-shift in its maximum absorption frequency. Earlier computational work explored the electrostatic influence of the highly charged RNA backbone and surrounding counterions for these asymmetrical changes in C-13 chemical shift. The work presented here examines the dynamical nature of the MAG molecule inside the RNA ligand-binding site using molecular dynamics with explicit solvent to explore the intermolecular and dynamic influences on the red-shift and to calculate the binding affinity. An induced fit behavior, similar to that caused by the electrostatic field alone, is observed. The binding strength of a series of malachite green derivatives correlates with the structural flatness of the ligand. These findings are important for the rational design of RNA ligands and for understanding the properties of RNA-ligand complexes.