The volume of the world's container transportation has been increasing. To serve this transportation need, the size of the container carrier is getting larger. The global ports are required to deepen the waterways as well as to prepare infrastructure to serve these super-size container carriers. However, few ports around the world could meet the requirements. To solve these difficulties, the concept of the Mobile Harbor has been developed. The semi-submersible (B1) type mobile harbor is still in the conceptual design stage. We need to predict the motion of the B1 type mobile harbor in the sea. WAMIT is one of the popular simulation programs for ship motion predictions. WAMIT can analyze wave interactions with offshore platforms and other structures of vessels. But, WAMIT has a simple method forcalculating viscous damping. For evaluating the motion of B1 type mobile harbor together with a container ship, we need to have the damping coefficient. The free decay test is one of methods of getting damping coefficient. We can use the damping coefficient from a free decay test as the imput to WAMIT simulation. To verify whether the simulation output is correct. the WAMIT output data has been compared with the 3D tank experiment data.