After a cMD production run has completed, the resulting trajectory can be analyzed using PyConSolv. This can be done in two ways, either using one of the provided shell scripts or using the python implementation present within PyConSolv. To obtain relevant conformers, the trajectory must be clustered. As we use a root mean square deviation (RMSD) of the distance of all heavy atoms as the clustering criteria, it is vital that the trajectory is properly aligned. This is resolved by aligning the solute based on a list of atom indices, provided by the user. The clustering can then be performed using one of the four methods provided by cpptraj: dbscan, hierarchical, kmeans or dpeaks . On the resulting clusters, single point calculations are performed, using the same electronic structure theory level that was used during the parametrization. Finally, a list of clusters, ranked by the single point energy, is presented to the user.