VMD was equipped with the option of loading BioMOCA structures. This is a very useful feature as one could load both the protein structure (i.e. PDB or PQR file) along with the structures generated by BioMOCA to make comparisons. Figure at the right shows how BioMOCA has generated a structure for Gramicidin channel with a membrane wrapped around it. Furthermore, BioMOCA also dumps the ion trajectories in standard formats so they could be later loaded to molecular visualization tools such as VMD and watched frame by frame in a movie format.