Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water
Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water
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DOI：
10.1016/j.cplett.2009.03.077
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发表时间：
2009-05-12
影响因子：
2.8
通讯作者：
Nakamura, Haruki
中科院分区：
文献类型：
--
作者：
Higo, Junichi;Kamiya, Narutoshi;Nakamura, Haruki
多正则分子动力学(MCMD)模拟是一种增强的构象采样方法。为了更加速采样，我们研究了一种轨迹并行化方法，该方法简单地将多个mcmd轨迹集成到一个轨迹中。这种方法大大减少了计算节点之间的通信。我们将这种方法应用于显性水中七个残基多肽的构象采样。在较宽的温度范围内，物理量与长期MCMD模拟得到的物理量很好地收敛。因此，积分可以在不执行长时间模拟的情况下生成正则系综。该方法适用于显性水中大量平行的长多肽(蛋白质)的折叠研究。(C)2009爱思唯尔B.V.保留所有权利。
Multicanonical molecular dynamics (McMD) simulation is an enhanced conformational sampling method. For more accelerated sampling, we examined a trajectory-parallelization method, which trivially integrates multiple McMD trajectories into one. This method decreases communications between computing nodes largely. We applied this method to conformational sampling of a seven-residue peptide in explicit water. Physical quantities converged well with those from a long McMD simulation in a wide temperature range. Thus, the integration can generate a canonical ensemble without performing the long simulation. The current method is useful for folding study of long polypeptides (proteins) in explicit water with massive parallelism. (c) 2009 Elsevier B.V. All rights reserved.