  Recent developments in specialized computer hardware have greatly accelerated
atomic level Molecular Dynamics (MD) simulations. A single GPU-attached cluster
is capable of producing microsecond-length trajectories in reasonable amounts
of time. Multiple protein states and a large number of microstates associated
with folding and with the function of the protein can be observed as
conformations sampled in the trajectories. Clustering those conformations,
however, is needed for identifying protein states, evaluating transition rates
and understanding protein behavior. In this paper, we propose a novel
data-driven generative conformation clustering method based on the adversarial
autoencoder (AAE) and provide the associated software implementation Cong. The
method was tested using a 208 microseconds MD simulation of the fast-folding
peptide Trp-Cage (20 residues) obtained from the D.E. Shaw Research Group. The
proposed clustering algorithm identifies many of the salient features of the
folding process by grouping a large number of conformations that share common
features not easily identifiable in the trajectory.
