TY - JOUR
T1 - Internal coordinate density of state from molecular dynamics simulation
AU - Lai, Pin Kuang
AU - Lin, Shiang Tai
N1 - Publisher Copyright:
© 2015 Wiley Periodicals, Inc.
PY - 2015/3/30
Y1 - 2015/3/30
N2 - 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.
AB - 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.
KW - Cartesian coordinates
KW - Density of state
KW - Internal coordinates
KW - Molecular dynamics simulation
KW - Normal modes
KW - Velocity spectrum
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U2 - 10.1002/jcc.23822
DO - 10.1002/jcc.23822
M3 - Article
AN - SCOPUS:84923352300
SN - 0192-8651
VL - 36
SP - 507
EP - 517
JO - Journal of Computational Chemistry
JF - Journal of Computational Chemistry
IS - 8
ER -