Photoswitchable Dronpa (psDronpa) is a unique member of the fluorescent protein family that can undergo reversible photoinduced switching between fluorescent and dark states and has recently been engineered into a dimer (pdDronpaV) that can dissociate and reassociate as part of its photoswitchable pathway. However, the specific details of the protein structure-function relationship of the dimer interface, along with how the dimer proteins interact with each other upon chromophore isomerization, are not yet clear. Classical molecular dynamics simulations were performed on psDronpa as monomers and dimers as well as the pdDronpaV dimer and with cis/trans chromophore structures. Analysis of the cis and trans isomers of the chromophore illustrated key differences between their interaction with residues in the protein in both the monomer and dimer forms of psDronpa. The chromophore was found to interact with water solvent uniquely in both monomeric and dimeric systems. Examination of the psDronpa dimer showed nonidentical chromophore interactions between the domains, indicating domain directional favoring. Examination of the trans form of pdDronpaV illuminated the importance of hydrogen bonding between the monomeric domains in maintaining their association as well as illustrating the motion of dissociation of the domains. This discovery offers important information for possible future mutations of pdDronpaV that might be made to accelerate dissociation.