  Controlling polymorphism in molecular crystals is crucial in the
pharmaceutical, dye, and pesticide industries. However, its theoretical
description is extremely challenging, due to the associated long timescales ($
> 1 \, \mu s$). We present an efficient procedure for identifying collective
variables that promote transitions between conformational polymorphs in
molecular dynamics simulations. It involves applying a simple dimensionality
reduction algorithm to data from short ($\sim ps$) simulations of the isolated
conformers that correspond to each polymorph. We demonstrate the utility of our
method in the challenging case of the important energetic material, CL-20,
which has three anhydrous conformational polymorphs at ambient pressure. Using
these collective variables in Metadynamics simulations, we observe transitions
between all solid polymorphs in the biased trajectories. We reconstruct the
free energy surface and identify previously unknown defect and intermediate
forms in the transition from one known polymorph to another. Our method
provides insights into complex conformational polymorphic transitions of
flexible molecular crystals.
