Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.
Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.
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DOI：
10.1021/ct9004068
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发表时间：
2010-03-09
影响因子：
5.5
通讯作者：
Scheraga, Harold A.
中科院分区：
文献类型：
--
作者：
Liwo, Adam;Oldziej, Stanislaw;Czaplewski, Cezary;Kleinerman, Dana S.;Blood, Philip;Scheraga, Harold A.
我们报告了我们的联合残基UNRES力场的实现，用于模拟大规模并行结构的蛋白质结构和动力学。除了我们以前的工作中已经实现的粗粒度并行，其中每个构象都由不同的任务处理，我们引入了一个细粒度级别，其中能量和梯度评估在几个任务之间分开。消息传递接口(MPI)库被用来构造并行代码。代码的并行性能已经在专业的Beowulf集群(至强四核)、一台Cray XT3超级计算机和两台具有正则分子动力学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，在256个处理器/轨迹的情况下，对于767个残基的单个轨迹，细粒部分的效率约为50%，速度提高了120倍。由于在快速自由度上进行平均，UNRES提供了与实验时间尺度相比有效的1000倍的速度，因此，使我们能够在挂钟时间的几天内有效地对含有500个或更多氨基酸残基的蛋白质进行毫秒尺度的模拟。
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 coarse-grained 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 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.
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