The String Method on collective variables finds minimum free energy paths (MFEP) between metastable states of a molecule. This requires choosing a set of reaction coordinates, or collective variables along which the transition takes place, which is non-trivial. In this paper we present a method for automatically extract- ing collective variables from low frequency instantaneous normal modes projected onto dihedral angles. We have applied this method to characterize isomerization transitions of alanine dipeptide. The algorithms we have developed are general and can be readily applied to larger systems. We also show that these collective variables simplify the String method and make it numerically more robust.