Internal coordinate density of state from molecular dynamics simulation
© 2015 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 36(2015), 8 vom: 30. März, Seite 507-17 |
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| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2015
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Cartesian coordinates density of state internal coordinates molecular dynamics simulation normal modes velocity spectrum |
| Zusammenfassung: | © 2015 Wiley Periodicals, Inc. 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 |
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| Beschreibung: | Date Completed 21.05.2015 Date Revised 24.02.2015 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
| ISSN: | 1096-987X |
| DOI: | 10.1002/jcc.23822 |