ACEMD：加速微秒级生物分子动力学
ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale
摘要：
近年来图形处理单元（GPU）的高运算性能和内在并行性为分子动力学模拟提供了技术优势。ACEMD是一个生产级的生物分子动力学（MD）模拟程序，专门为GPU设计，能够为具有超过23，000个原子的全原子蛋白质系统实现40纳秒/天的超级计算规模性能。我们说明了代码的特点，它的验证和性能。我们还运行了一个微秒长的轨迹为全原子分子系统在明确的TIP 3 P水在一个工作站上的计算机配备只有3个GPU。这种高性价比的硬件性能使ACEMD能够达到微秒级的时间尺度，这在科学应用方面具有重要意义。
英文摘要：
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.
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