Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
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DOI：
10.1063/1.4793625
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发表时间：
2013-03-07
影响因子：
4.4
通讯作者：
Vendruscolo, Michele
中科院分区：
文献类型：
--
作者：
Cavalli, Andrea;Camilloni, Carlo;Vendruscolo, Michele
为了模拟蛋白质的动力学行为，一种行之有效的方法是将实验参数作为复制平均结构约束引入分子动力学模拟中。在这里，我们证明这种方法的情况下，质子间的距离信息所提供的核Overhauser效应表明，它产生合奏的构象根据最大熵原理。这些结果表明，在分子动力学模拟中使用复制平均的结构约束，给定的力场和一组实验数据，可以提供一个准确的近似未知的玻尔兹曼分布的系统。(C)2013年美国物理学会。[http：//dx.doi.org/10.1063/1.4793625]
In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4793625]