A CUDA based solute interaction calculation of biomolecular simulation for GROMOS

Molecular dynamics is an important computational tool to simulate and understand biochemical processes at atomic level. However, large system simulations with many atoms and numerous time steps require huge amount of calculation and in traditional CPU, it is time-consuming. During the past few years, graphics processing units have become an important computing platform in many scientific fields, especially in high performance computing community. In this paper,implementation of solute-solute and solute-solvent interaction calculation with NVIDIA´s Tesla C1060 will be presented. Therefore, the implementation enables users of GROMOS software for biomolecular simulation to run the whole nonbonded interaction evaluation on the GPU. Our experimental results are ten to twenty times faster than the conventional sequential implementation running on the CPU core.