基于图形处理器的生物分子朗之万动力学模拟
Langevin dynamics simulations of biomolecules on graphics processors
摘要：
由于所涉及的时间尺度非常长（us-s），在生理相关条件下，基本生物过程（包括生物分子的折叠、错误折叠和机械解开）的理论建模即使对于分布式计算系统也具有挑战性。图形处理单元（GPU）正在成为更传统的CPU的替代编程平台，因为它们提供可以在广泛的科学应用中使用的高原始计算能力。使用粗粒度的自组织聚合物（SOP）模型，我们已经开发并测试了基于GPU的实现Langevin模拟蛋白质（SOP-GPU程序）。使用基于粒子或基于交互对的并行化实现所有粒子的力的同时计算，与程序的优化CPU版本相比，这导致约30倍的加速。我们评估了SOP-GPU程序的端到端应用程序的计算性能，其中算法的所有步骤都在GPU上运行，通过分析一些小蛋白质，长蛋白质纤维和大尺寸蛋白质组装体的相关模拟时间和内存使用情况。SOP-GPU软件包现在可以用于大尺寸蛋白质系统力学性能的理论探索，生成施力实验条件下的力延伸和力压痕曲线，并关联单分子实验结果体外和计算机模拟。
英文摘要：
Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging even for distributed computing systems. Graphics Processing Units (GPUs) are emerging as an alternative programming platform to the more traditional CPUs as they provide high raw computational power that can be utilized in a wide range of scientific applications. Using a coarse-grained Self Organized Polymer (SOP) model, we have developed and tested the GPU-based implementation of Langevin simulations for proteins (SOP-GPU program). Simultaneous calculation of forces for all particles is implemented using either the particle based or the interacting pair based parallelization, which leads to a ~30-fold acceleration compared to an optimized CPU version of the program. We assess the computational performance of an end-to-end application of the SOP-GPU program, where all steps of the algorithm are running on the GPU, by profiling the associated simulation time and memory usage for a number of small proteins, long protein fibers, and large-size protein assemblies. The SOP-GPU package can now be used in the theoretical exploration of the mechanical properties of large-size protein systems to generate the force-extension and force-indentation profiles under the experimental conditions of force application, and to relate the results of single-molecule experiments in vitro and in silico.
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