Multiscale macromolecular simulation: role of evolving ensembles.
Multiscale macromolecular simulation: role of evolving ensembles.
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DOI：
10.1021/ci3002952
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发表时间：
2012-10-22
影响因子：
5.6
通讯作者：
Ortoleva PJ
中科院分区：
文献类型：
--
作者：
Singharoy A;Joshi H;Ortoleva PJ
多尺度分析提供了一种有效的模拟大分子组装的算法。该算法涉及的准平衡概率密度的原子配置和朗之万动力学的空间粗粒度的变量表示的顺序参数（OP）表征纳米系统的功能的协同进化。在实践中，概率密度的实现涉及到原子配置的常数OP系综的生成。此类系综用于构建介导随机OP动态的热力和扩散因子。在每一个朗之万时间步生成全原子系综在计算上是昂贵的。在这里，多尺度计算的大分子系统是更有效的方法，自洽折叠在合奏的所有原子配置中构建的早期步骤，历史，朗之万演化。这个过程占这些合奏的时间演变，准确地提供热力和扩散。结果表明，基于OP的模拟的效率和准确性增加，通过整合这些历史信息。准确性随着计算中包含的历史时间步数的平方根而提高。因此，CPU使用率可以减少3-8倍，而不会损失精度。该算法实现到我们现有的力场为基础的多尺度仿真平台，并通过病毒衣壳的结构动力学证明。
Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin timestep is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.
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影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
DOI：
10.1016/j.pbiomolbio.2011.07.006
发表时间：
2011-10
影响因子：
3.8
作者：
Joshi H;Singharoy A;Sereda YV;Cheluvaraja SC;Ortoleva PJ
通讯作者：
Ortoleva PJ
影响因子：
5.4
作者：
CHRISTENSEN, ND;KREIDER, JW
通讯作者：
KREIDER, JW
影响因子：
4.1
作者：
ERMAK, DL;BUCKHOLZ, H
通讯作者：
BUCKHOLZ, H
影响因子：
1.9
作者：
Kadau, Kai;Germann, Timothy C.;Lomdahl, Peter S.
通讯作者：
Lomdahl, Peter S.