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Internal coordinate density of state from molecular dynamics simulation.

Pin-Kuang Lai1, Shiang-Tai Lin

  • 1Department of Chemical Engineering, National Taiwan University, Taipei, 10617, Taiwan.

Journal of Computational Chemistry
|January 8, 2015
PubMed
Summary

Calculating vibrational density of states (DoS) using internal coordinates accurately identifies molecular motions. This method distinguishes free rotations from hindered ones, offering clearer insights into system dynamics.

Keywords:
Cartesian coordinatesdensity of stateinternal coordinatesmolecular dynamics simulationnormal modesvelocity spectrum

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Spectroscopy

Background:

  • Vibrational density of states (DoS) reveals system structure and dynamics.
  • Cartesian coordinate-based DoS can misinterpret vibrational modes, especially free rotations.
  • Macromolecular DoS often shows artificial low-frequency enhancements due to coupled motions.

Purpose of the Study:

  • To develop a method for accurate identification of vibrational modes.
  • To differentiate between free and hindered rotational motions.
  • To provide clearer insights into the dynamic behavior of molecular systems.

Main Methods:

  • Calculating DoS from the Fourier transform of the velocity autocorrelation function.
  • Utilizing internal coordinates for DoS calculation.
  • Employing a generalized Wilson's B-matrix to convert Cartesian velocities to internal coordinates.

Main Results:

  • DoS in internal coordinates correctly identifies free dihedral rotations.
  • Distinguishes free rotations from hindered rotations, unlike Cartesian DoS.
  • Attributes low-frequency modes in Cartesian DoS of macromolecules to coupled dihedral and angle motions.

Conclusions:

  • Internal coordinate DoS accurately deconvolutes molecular internal motions.
  • Provides more fruitful insights into system dynamic behaviors compared to Cartesian DoS.
  • Enhances the analysis of molecular dynamics and vibrational properties.