by James C. Phillips and John E. Stone, ACM Queue
Computer simulation has become an integral part of the study of the structure and function of biological molecules. For years, parallel computers have been used to conduct these computationally demanding simulations and to analyze their results. These simulations function as a “computational microscope,” allowing the scientist to observe details of molecular processes too small, fast, or delicate to capture with traditional instruments. Over time, commodity GPUs (graphics processing units) have evolved into massively parallel computing devices, and more recently it has become possible to program them in dialects of the popular C/C++ programming languages.
This has created a tremendous opportunity to employ new simulation and analysis techniques that were previously too computationally demanding to use. In other cases, the computational power provided by GPUs can bring analysis techniques that previously required computation on HPC (high-performance computing) clusters down to desktop computers, making them accessible to application scientists lacking experience with clustering, queuing systems, and the like.
This article is based on our experiences developing software for use by and in cooperation with scientists, often graduate students, with backgrounds in physics, chemistry, and biology.
