Molecular dynamics simulations were performed to study the self-assembly of a spherical complex through metal ligand coordination interactions. M6L8, a nanosphere with six palladium ions and eight pyridine-capped tridentate ligands, was selected as a target system. We successfully observed the spontaneous formation of spherical shaped M6L8 cages over the course of our simulations, starting from random initial placement of the metals and ligands. To simulate spontaneous coordination bond formations and breaks, the cationic dummy atom method was employed to model nonbonded metal ligand interactions. A coarse-grained solvent model was used to fill the gap between the time scale of the supramolecular self-assembly and that accessible by common molecular dynamics simulation. The simulated formation process occurred in the distinct three-stage (assembly, evolution, fixation) process that is well correlated with the experimental results. We found that the difference of the lifetime (or the ligand exchange rate) between the smaller-sized incomplete clusters and the completed M6L8 nanospheres is crucially important in their supramolecular self-assembly.