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Extracting effective normal modes from equilibrium dynamics at finite temperature
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10.1063/1.2346678
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    Affiliations:
    1 Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, Paris 6, UMR 7600, Tour 24-25, 2ème Étage, 4 Place Jussieu, F-75005 Paris, France
    2 Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, Paris 6, UMR 7600, Tour 24-25, 2ème Étage, 4 Place Jussieu, F-75005 Paris, France and Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry val d’Essonne, UMR 8587, Rue Père A. Jarland, F-91025 Evry, France
    3 Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry val d’Essonne, UMR 8587, Rue Père A. Jarland, F-91025 Evry, France
    4 Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, Paris 6, UMR 7600, Tour 24-25, 2ème Étage, 4 Place Jussieu, F-75005 Paris, France
    a) Electronic mail: vuilleum@lptl.jussieu.fr
    J. Chem. Phys. 125, 144106 (2006); http://dx.doi.org/10.1063/1.2346678
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View: Figures

Figures

Image of FIG. 1.
FIG. 1.

(Color) Power spectra of the effective normal modes of at in the Eckart framework rotating with the molecule (color lines) and the eigenvalues of the Hessian at (vertical line with a cross at the top).

Image of FIG. 2.
FIG. 2.

(Color) Effective normal modes (blue arrows) at and normal modes (red arrows) of . Modes have increasing frequency from left to right and top to bottom.

Image of FIG. 3.
FIG. 3.

(Color) Power spectra of the effective normal modes in the rotating Eckart frame (a) and in the laboratory frame using the coordinate system of the Eckart frame (b) (see text). In both frames, the solid red curve corresponds to the power spectrum of the water bending mode, while the green curve and the black solid curves correspond to the power spectra of the symmetric and asymmetric stretches, respectively. In (b), the blue curves represent the power spectra of water translation modes (solid: translation perpendicular to the molecular plane, dashed: translation along the HH vector, dotted: translation along the OHO bisectrix), while the pink curves represent the power spectra of the librational modes (solid: rotation in the molecular plane, dashed and dotted: rotation around the two OH axes).

Image of FIG. 4.
FIG. 4.

(Color) Effective normal modes of a water molecule in liquid water (bend, symmetric and asymmetric stretches), in the Eckart frame (blue arrows), and in the coordinate system associated to the Eckart frame (red arrows).

Image of FIG. 5.
FIG. 5.

(Color) A ball and stick representation of the uracil molecule. Hydrogen atoms are white, carbon cyan, nitrogen are blue, and oxygen atoms are in red.

Image of FIG. 6.
FIG. 6.

(Color) Power spectra of the effective normal modes of one uracil molecule in aqueous solution between 1000 and .

Image of FIG. 7.
FIG. 7.

(Color) Effective normal modes of one uracil molecule in aqueous solution between 1000 and .

Image of FIG. 8.
FIG. 8.

(Color) Effective normal modes of one uracil molecule in aqueous solution between 1400 and .

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/content/aip/journal/jcp/125/14/10.1063/1.2346678
2006-10-11
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Extracting effective normal modes from equilibrium dynamics at finite temperature
http://aip.metastore.ingenta.com/content/aip/journal/jcp/125/14/10.1063/1.2346678
10.1063/1.2346678
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