Macromolecular Entropy Can Be Accurately Computed from Force
Macromolecular Entropy Can Be Accurately Computed from Force
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DOI：
10.1021/ct500684w
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发表时间：
2014-11-01
影响因子：
5.5
通讯作者：
Henchman, Richard H.
中科院分区：
文献类型：
--
作者：
Hensen, Ulf;Graeter, Frauke;Henchman, Richard H.
提出了一种由分子动力学模拟中计算的原子力计算分子熵的方法。具体地说，质量加权力协方差矩阵的对角化产生了在谐和近似下可以与振动频率相关的特征值。每个振动模的谐振子熵可以相加，从而得到总熵。对一系列碳氢化合物、二烷基和β发夹的计算结果与热力学积分值的一致性比用准谐分析计算的结果要好得多。研究发现，力更接近于调和分布，而不是坐标位移，并且更好地捕捉到潜在的势能面。这种方法的精度、简单性和与拟谐分析的计算相似性，只需要输入作用力轨迹而不是坐标轨迹，使得它很容易适用于广泛的问题。
A method is presented to evaluate a molecules entropy from the atomic forces calculated in a molecular dynamics simulation. Specifically, diagonalization of the mass-weighted force covariance matrix produces eigenvalues which in the harmonic approximation can be related to vibrational frequencies. The harmonic oscillator entropies of each vibrational mode may be summed to give the total entropy. The results for a series of hydrocarbons, dialanine and a beta hairpin are found to agree much better with values derived from thermodynamic integration than results calculated using quasiharmonic analysis. Forces are found to follow a harmonic distribution more closely than coordinate displacements and better capture the underlying potential energy surface. The methods accuracy, simplicity, and computational similarity to quasiharmonic analysis, requiring as input force trajectories instead of coordinate trajectories, makes it readily applicable to a wide range of problems.