期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 36, 期 8, 页码 507-517出版社
WILEY-BLACKWELL
DOI: 10.1002/jcc.23822
关键词
density of state; velocity spectrum; Cartesian coordinates; internal coordinates; normal modes; molecular dynamics simulation
资金
- National Science Council of Taiwan [NSC 101-2628-E-002-014-MY3]
The vibrational density of states (DoS), calculated from the Fourier transform of the velocity autocorrelation function, provides profound information regarding the structure and dynamic behavior of a system. However, it is often difficult to identify the exact vibrational mode associated with a specific frequency if the DoS is determined based on velocities in Cartesian coordinates. Here, the DoS is determined based on velocities in internal coordinates, calculated from Cartesian atomic velocities using a generalized Wilson's B-matrix. The DoS in internal coordinates allows for the correct detection of free dihedral rotations that may be mistaken as hindered rotation in Cartesian DoS. Furthermore, the pronounced enhancement of low frequency modes in Cartesian DoS for macromolecules should be attributed to the coupling of dihedral and angle motions. The internal DoS, thus deconvolutes the internal motions and provides fruitful insights to the dynamic behaviors of a system. (c) 2015 Wiley Periodicals, Inc.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据