Gaudin F, Lancelot G, Genest D
Centre de Biophysique Moleculaire, CNRS, Orleans, France.
J Biomol Struct Dyn. 1997 Oct;15(2):357-67. doi: 10.1080/07391102.1997.10508198.
A strategy is presented for searching which atoms can be regrouped within rigid sub-units during the time course of Molecular Dynamics simulations of biopolymers. The root mean square fluctuations of the interatomic distances are used as a criterion. The number of rigid sub-units which are found depends on the tolerance rc for the definition of a rigid body, i.e. until which value the fluctuations can be neglected. The method is applied to two self-complementary oligonucleotides belonging to the B-form family which give identical results. With rc = 0.027 nm each nucleotide may be described as 3 rigid sub-units: the sugar ring, the base and the backbone (PO4 + C5' atoms). With rc = 0.01 nm, the same sub-units are obtained except that C5' can no more be regrouped with the PO4 atoms. It is shown that the variation of the coulombic potential owing to the deformation of the sub-units during the time course of the simulation is on the same order of magnitude as the inaccuracy due to the choice of the force field parameters.
本文提出了一种策略，用于在生物聚合物分子动力学模拟过程中搜索哪些原子可以在刚性亚基内重新组合。原子间距离的均方根波动被用作一个标准。所发现的刚性亚基数量取决于刚体定义的容差rc，即波动可被忽略的直到该值。该方法应用于属于B型家族的两个自互补寡核苷酸，得到了相同的结果。当rc = 0.027 nm时，每个核苷酸可被描述为3个刚性亚基：糖环、碱基和主链（PO4 + C5'原子）。当rc = 0.01 nm时，得到相同的亚基，只是C5'不能再与PO4原子重新组合。结果表明，在模拟过程中由于亚基变形导致的库仑势变化与由于力场参数选择导致的不准确性处于同一数量级。
