General Purpose Graphics Processing Unit (GPGPU) is recently applied for High Performance Computing (HPC). We can obtain rapidly increasing computational power from GPGPU cluster.
We optimized MD simulation program on GPGPU cluster. In our presentation, we will show performances of some proteins. On the other hand, we developed the binding free energy calculation system based on molecular dynamics simulation. The binding free energy is important information for understanding interactions between protein and protein or protein and chemical compounds. We also show calculation results of the binding free energy of some targets.