Extracting parameters for base-pair level models of DNA from molecular dynamics simulations
Extracting parameters for base-pair level models of DNA from molecular dynamics simulations
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DOI：
10.1007/s002140100256
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发表时间：
2001-06-01
影响因子：
1.7
通讯作者：
Maddocks, JH
中科院分区：
文献类型：
--
作者：
Gonzalez, O;Maddocks, JH
描述了一种从分子动力学 (MD) 模拟中提取 DNA 刚性碱基对模型的完整序列相关能量参数集的方法。该方法与平衡统计力学完全一致，并得出碱基对单元的有效惯性参数以及碱基对连接的堆叠和刚度参数。我们给出了明确的公式，可以根据平衡平均值生成一整套碱基对模型参数，这些参数可以根据 MD 模拟中生成的时间序列进行估计。要平均的表达式在很大程度上取决于用于描述刚体方向的坐标的选择以及每个连接处应变测量的选择。
A method is described to extract a complete set of sequence-dependent energy parameters for a rigid base-pair model of DNA from molecular dynamics (MD) simulations. The method is properly consistent with equilibrium statistical mechanics and leads to effective inertia parameters for the base-pair units as well as stacking and stiffness parameters for the basepair junctions. We give explicit formulas that yield a complete set of base-pair model parameters in terms of equilibrium averages that can be estimated from a time series generated in an MD simulation. The expressions to be averaged depend strongly both on the choice of coordinates used to describe rigid-body orientations and on the choice of strain measures at each junction.