Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.
Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.
复制标题
通过异步复制品交换模拟表征尿嘧啶核糖核苷的三维自由能流形。
DOI：
10.1021/ct500776j
复制
发表时间：
2015
影响因子：
5.5
通讯作者：
York,DarrinM
中科院分区：
文献类型：
--
作者：
Radak,BrianK;Romanus,Melissa;Lee,Tai-Sung;Chen,Haoyuan;Huang,Ming;Treikalis,Antons;Balasubramanian,Vivekanandan;Jha,Shantenu;York,DarrinM
交换分子动力学已经成为一个强大的工具，有效地采样自由能景观的构象和化学转变。然而，在有效地让这样的模拟扩展到非常大量的副本，以解决超过两个维度的状态空间中的问题，仍然存在艰巨的挑战。进行这种模拟的技术的发展还处于起步阶段，因此，哪些应用需要扩展到更高的维度仍然是一个悬而未决的问题。在目前的工作中，我们探索这个问题的空间，通过应用异步哈密顿副本交换分子动力学结合量子力学/分子力学势探索一个简单的核糖核苷的构象空间。这是通过使用新开发的软件框架来完成的，该软件框架能够执行> 3，000个副本，而资源仅足以同时运行2，000个副本。这对于传统的同步副本交换方法可能是不可能的。我们的研究结果表明：（1）生物系统的高维采样模拟的必要性，甚至简单到单个核糖核苷，以及2.）异步交换协议在管理高维采样模拟中预期的同时资源需求中的效用。预计更复杂的系统只会增加计算需求和复杂性，因此报告的异步方法可能会越来越有益，以便使这些应用程序可用于广泛的计算科学家。
Replica exchange molecular dynamics has emerged as a powerful tool for efficiently sampling free energy landscapes for conformational and chemical transitions. However, daunting challenges remain in efficiently getting such simulations to scale to the very large number of replicas required to address problems in state spaces beyond two dimensions. The development of enabling technology to carry out such simulations is in its infancy, and thus it remains an open question as to which applications demand extension into higher dimensions. In the present work, we explore this problem space by applying asynchronous Hamiltonian replica exchange molecular dynamics with a combined quantum mechanical/molecular mechanical potential to explore the conformational space for a simple ribonucleoside. This is done using a newly developed software framework capable of executing >3,000 replicas with only enough resources to run 2,000 simultaneously. This may not be possible with traditional synchronous replica exchange approaches. Our results demonstrate 1.) the necessity of high dimensional sampling simulations for biological systems, even as simple as a single ribonucleoside, and 2.) the utility of asynchronous exchange protocols in managing simultaneous resource requirements expected in high dimensional sampling simulations. It is expected that more complicated systems will only increase in computational demand and complexity, and thus the reported asynchronous approach may be increasingly beneficial in order to make such applications available to a broad range of computational scientists.
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增强的采样算法。
影响因子：
--
作者：
A. Mitsutake;Yoshiharu Mori;Y. Okamoto
通讯作者：
Y. Okamoto
极限科学与工程发现环境会议论文集：发现之门
DOI：
--
发表时间：
2013
期刊：
影响因子：
--
作者：
Nancy Wilkins
通讯作者：
Nancy Wilkins
影响因子：
5.5
作者：
Wallace JA;Shen JK
通讯作者：
Shen JK
影响因子：
5.5
作者：
Jiang, Wei;Roux, Benoit
通讯作者：
Roux, Benoit
影响因子：
4.4
作者：
Shirts, Michael R.;Chodera, John D.
通讯作者：
Chodera, John D.