AMBER 11, the latest version of one of the most widely used applications for biochemists and others involved in molecular dynamics research, is optimized to run on NVIDIA® graphics processing units (GPUs), which speed up the tool by up to 100-fold over a traditional CPU -based server. GPUs deliver performance from a desktop workstation that previously could only be achieved on a supercomputer, improving productivity as scientists no longer need to wait for time on a shared supercomputer or departmental cluster of servers.
…AMBER 11 is designed to take advantage of NVIDIA Tesla™ 20-series GPUs, which utilize the massively parallel CUDA™ architecture for the specific needs of high performance computing applications. In early trials with the AMBER user community, Dr. Walker received over a dozen reports of speedups over 30-times on a range of bio-molecular simulations.
…Dr. Walker noted that just one Tesla GPU provides as much processing power as a high performance cluster of 512 CPU cores when simulating one nanosecond in the lifetime of a 25,000 atom implicit solvent nucleosome. In a simpler explicit solvent simulation, such as the JAC benchmark, he noted that one Tesla GPU provides the equivalent processing power of 48 cores of the NSF Ranger supercomputer.