AMBER RESEARCH CODE GETS IMPRESSIVE GAINS WITH NVIDIA CUDA

by Linda Barney

In his talk in NVIDIA’s theater, Ross Walker described the research being done by the San Diego Supercomputer Center (SDSC) and how NVIDIA GPUs are helping with this research.  The SDSC team performs research on biomolecules, biofuels, and flu viruses.

“My current research is directed towards developing new molecular dynamics techniques for studying protein reactivity and reaction pathways with the goal of furthering the understanding of such complex mechanistic processes in order to aid the development of new drugs and to improve current biofuel technologies,” states Walker. The research involves high speed simulations using AMBER, a widely used package of molecular simulation programs, used to study the dynamics of biomolecules.

SDSC is using computers running NVIDIA’s Tesla GPUs in their research. Walker reports that “The NVIDIA CUDA architecture accelerates AMBER simulations by up to 100  times when compared with a CPU.”

In addition, using GPUs has changed how research is done. Traditionally, researchers had to submit simulations to a queue and had to wait several hours or up to 2 or 3 days for the results. If there was a problem during the run, then the work had to start all over. With desktop computers using NVIDIA Tesla GPUs and CUDA software, researchers can run simulations and see the results quickly. “Using NVIDIA tools allows SDSC researchers to complete simulations in a reasonable time, we can work interactively with the data, see results quickly and make modifications in a reasonable timeframe,” states Walker.