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首页> 外文期刊>Journal of chemical theory and computation: JCTC >Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics

机译：大规模并行系统上粗粒度UNRES力场的分子动力学及其扩展的实现：蛋白质结构，动力学和热力学的毫秒级模拟

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摘要

We report the implementation of our united-residue UNRES force field for simulations of protein structure and dynamics with massively parallel architectures. In addition to coarsegrained parallelism already implemented in our previous work, in which each conformation was treated by a different task, we introduce a fine-grained level in which energy and gradient evaluation are split between several tasks. The Message Passing Interface (MPI) libraries have been utilized to construct the parallel code. The parallel performance of the code has been tested on a professional Beowulf cluster (Xeon Quad Core), a Cray XT3 supercomputer, and two IBM BlueGene/P supercomputers with canonical and replica-exchange molecular dynamics. With IBM BlueGene/P, about 50% efficiency and a 120-fold speed-up of the fine-grained part was achieved for a single trajectory of a 767-residue protein with use of 256 processors/trajectory. Because of averaging over the fast degrees of freedom, UNRES provides an effective 1000-fold speed-up compared to the experimental time scale and, therefore, enables us to effectively carry out millisecond-scale simulations of proteins with 500 and more amino acid residues in days of wall-clock time.
机译：我们报告了联合残基UNRES力场的实施情况，该场用于模拟具有大规模并行体系结构的蛋白质结构和动力学。除了在我们先前的工作中已经实现的粗粒度并行度（其中每个构象都由一个不同的任务处理）之外，我们还引入了一个细粒度的级别，其中能量和梯度评估被划分为多个任务。消息传递接口（MPI）库已用于构造并行代码。该代码的并行性能已在专业的Beowulf集群（至强四核），一台Cray XT3超级计算机以及两台具有规范和副本交换分子动力学的IBM BlueGene / P超级计算机上进行了测试。使用IBM BlueGene / P，使用256个处理器/轨迹对767个残基蛋白的单个轨迹实现了约50％的效率和120倍的细粒部分加速。由于对快速自由度求平均，与实验时间尺度相比，UNRES可以有效地提高1000倍的速度，因此，使我们能够有效地对具有500个或更多氨基酸残基的蛋白质进行毫秒尺度的模拟。挂钟时间的天数。

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