Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties.
Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties.
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DOI：
10.1021/ct900373z
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发表时间：
2009-12-08
影响因子：
5.5
通讯作者：
McCammon, J. Andrew
中科院分区：
文献类型：
--
作者：
Baron, Riccardo;Huenenberger, Philippe H.;McCammon, J. Andrew
用微秒级分子动力学模拟方法研究了肽测试系统的绝对单分子构型熵及其修正项的收敛性质。与以前的应用程序的不同化学性质的系统的结果进行比较。结果表明，（i）非谐性的影响是小的，（ii）成对相关性的影响通常是大的，和（iii）后者在更大程度上影响的熵估计的热力学状态，其特征在于由较高的运动相关性。这种偏离准谐波行为的原因进行了解释。这种改进的方法也提供熵的分子系统经历构象转变，其特征在于高度受挫的能量表面，因此不限于系统采样一个单一的准谐波盆地。总体而言，这项研究强调需要广泛的相空间采样，以获得一个可靠的估计熵的贡献。
The convergence properties of the absolute single-molecule configurational entropy and the correction terms used to estimate it are investigated using microsecond molecular dynamics simulation of a peptide test system and an improved methodology. The results are compared with previous applications for systems of diverse chemical nature. It is shown that (i) the effect of anharmonicity is small, (ii) the effect of pairwise correlation is typically large, and (iii) the latter affects to a larger extent the entropy estimate of thermodynamic states characterized by a higher motional correlation. The causes of such deviations from a quasi-harmonic behavior are explained. This improved approach provides entropies also for molecular systems undergoing conformational transitions and characterized by highly frustrated energy surfaces, thus not limited to systems sampling a single quasi-harmonic basin. Overall, this study emphasizes the need for extensive phase-space sampling in order to obtain a reliable estimation of entropic contributions.
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