14:30 GPU based Molecular Dynamics Simulation: acceleration and its application – M. Sekijima (Tokyo Tech)

Molecular dynamics (MD) simulations are widely used for simulating molecular motion for gaining a deeper understanding of chemical reactions, fluid flow, phase transitions, and other physical phenomena due to molecular interactions. This simulation of a continuous process is broken down into discrete small timesteps, each of which is an iteration of two parts: force calculation (calculating the forces from the evaluated conformational energies) and atom update (calculating new coordinates of the molecules).

 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.