A SAMPLING PROBLEM IN MOLECULAR-DYNAMICS SIMULATIONS OF MACROMOLECULES
A SAMPLING PROBLEM IN MOLECULAR-DYNAMICS SIMULATIONS OF MACROMOLECULES
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DOI：
10.1073/pnas.92.8.3288
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发表时间：
1995-04-11
影响因子：
11.1
通讯作者：
PHILLIPS, GN
中科院分区：
文献类型：
--
作者：
CLARAGE, JB;ROMO, T;PHILLIPS, GN
分子动力学模拟预测的1ns量级的低频原子位移的相关性对于目前可通过该技术获得的时间尺度来说是欠采样的。这是用大分子中波动的三种不同表示来显示的：使用漫射x射线散射数据的晶体学的倒数空间，使用原子位移的协方差矩阵的真实三维笛卡尔空间，以及使用维数减少的投影来可视化相空间采样的程度的蛋白质的3n维构型空间。
Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.