Abstract: The chloridion transporter，EcClC，is a homodimer, which consists of two similar monomers. Based on the experiment of homodimer separation, with molecule dynamic simulation, the writer mutated two smaller and nonpolar residues (isoleucine) into two bigger and aromatic residues (tryptophan). In the simulation process, the writer calculated the contact area，the number of Hbond，the potential deviations of vdw and electricity between chain A and chain B，and the all had varying degrees of change. The most obverse change is the contact area between chain A and chain B.

Key words: chloridion transporter, molecule dynamic simulation, separation of homodimer, microprocess