Compared with traditional ionic liquids, ionic liquids based on collinium cations have special properties such as high biodegradability, low toxicity and low synthesis cost. In addition to experimental studies, molecular simulations play a significant role in understanding the molecular processes of this class of ionic liquids. In this work, a large-scale simulation method (particle dissipative dynamics simulation) has been used to study the structural properties of these ionic liquids. By developing a coarse-grained model of ionic liquids containing collinium cations and anions derived from amino acids (alanine, valine, isoleucine, norvaline, norleucine, leucine, phenylalanine, histidine, proline, cysteine, threonine), the particle dissipative dynamics parameters have been extracted. Then, by performing particle dissipative dynamics simulations, the density and microscopic structure of these ionic liquids have been calculated and compared with the values obtained from atomistic simulations.