Metropolis算法在蛋白质动力学模拟中的应用 链条

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摘要翻译：
Monte Carlo算法的Metropolis实现被用来研究多体系统的平衡热力学。选择小试步，应用该算法得到的轨迹与Langevin动力学得到的轨迹一致。将此过程应用于一个简化的蛋白质模型，可以证明在一个Monte Carlo步骤中对蛋白质主链二面体的运动设置1度阈值，与非平衡动力学相关的平均量（如能量、RMSD等）可以很好地再现，而较高矩的良好描述需要较小的运动。一个重要的结果是蒙特卡罗步骤的持续时间与温度成线性关系，这是在不同温度下进行模拟时应该考虑的。
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英文标题：
《Use of the Metropolis algorithm to simulate the dynamics of protein
  chains》
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作者：
G. Tiana, L. Sutto and R. A. Broglia
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最新提交年份：
2007
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分类信息：

一级分类：Quantitative Biology        数量生物学
二级分类：Other Quantitative Biology        其他定量生物学
分类描述：Work in quantitative biology that does not fit into the other q-bio classifications
不适合其他q-bio分类的定量生物学工作
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英文摘要：
  The Metropolis implementation of the Monte Carlo algorithm has been developed to study the equilibrium thermodynamics of many-body systems. Choosing small trial moves, the trajectories obtained applying this algorithm agree with those obtained by Langevin's dynamics. Applying this procedure to a simplified protein model, it is possible to show that setting a threshold of 1 degree on the movement of the dihedrals of the protein backbone in a single Monte Carlo step, the mean quantities associated with the off-equilibrium dynamics (e.g., energy, RMSD, etc.) are well reproduced, while the good description of higher moments requires smaller moves. An important result is that the time duration of a Monte Carlo step depends linearly on the temperature, something which should be accounted for when doing simulations at different temperatures.
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PDF链接：
https://arxiv.org/pdf/q-bio/0606038

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关键词：Metropolis Metro Polis Etro 动力学 Metropolis obtained Langevin dynamics 研究