All-Atom Normal Mode Calculations of Large Molecular Systems Using Iterative Methods

Author(s):  
Liliane Mouawad ◽  
David Perahia
2009 ◽  
Vol 23 (31) ◽  
pp. 5819-5834 ◽  
Author(s):  
OLCAY ÜZENGI AKTÜRK ◽  
OĞUZ GÜLSEREN ◽  
MEHMET TOMAK

Although the stable structures and other physical properties of small Ag n and Au n, were investigated in the literature, phonon calculations are not done yet. In this work, we present plane-wave pseudopotential calculations based on density-functional formalism. The effect of using the generalized gradient approximation (GGA) and local density approximation (LDA) to determine the geometric and electronic structure and normal mode calculations of Ag n and Au n, is studied up to eight atoms. Pure Au n and Ag n clusters favor planar configurations. We calculated binding energy per atom. We have also calculated the normal mode calculations and also scanning tunneling microscope (STM) images for small clusters for the first time.


1999 ◽  
Vol 110 (21) ◽  
pp. 10410-10422 ◽  
Author(s):  
Robert L. Murry ◽  
John T. Fourkas ◽  
Wu-Xiong Li ◽  
Tom Keyes

1982 ◽  
Vol 72 (2) ◽  
pp. 505-509 ◽  
Author(s):  
M. C. Ferla ◽  
F. B. Jensen ◽  
W. A. Kuperman

2018 ◽  
Author(s):  
Daniel R. Moberg ◽  
Peter J. Sharp ◽  
Francesco Paesani

<div> <div> <div> <p>We build on results from our previous investigation into ice Ih using a combination of classical many-body molecular dynamics (MB-MD) and normal mode (NM) calculations to obtain molecular level information on the spectroscopic signatures in the OH stretching region for all seven of the known ordered crystalline ice phases. The classical MB-MD spectra are shown to capture the important spectral features by comparing with experimental Raman spectra. This motivates the use of the classical simulations in understanding the spectral features of the various ordered ice phases in molecular terms. This is achieved through NM analysis to first demonstrate that the MB-MD spectra can be well recovered through the transition dipole moments and polarizability tensors calculated from each NM. From the normal mode calculations, measures of the amount of symmetric and antisymmetric stretching are calculated for each ice, as well as an approximation of how localized each mode is. These metrics aid in viewing the ice phases on a continuous spectrum determined by their density. As in ice Ih, it is found that most of the other ordered ice phases have highly delocalized modes and their spectral features cannot, in general, be described in terms of molecular normal modes. The lone exception is ice VIII, the densest crystalline ice phase. Despite being found only at high pressure, the symmetry index shows a clear separation of symmetric and antisymmetric stretching modes giving rise to two distinct features. </p> </div> </div> </div>


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