Effective numbers of modes applied to analysis of internal dynamics of weakly bound clusters

J Chem Phys. 2010 Oct 14;133(14):144101. doi: 10.1063/1.3496375.

Abstract

The dependence of the volume of the chaotic component in the internal dynamics of triatomic van der Waals clusters on the angular momentum is calculated using the Monte Carlo and molecular dynamics methods. It has been found that this dependence is nonmonotonic and that its functional form varies for different values of the total energy. The effective number of rotational modes was used to clarify why a change in the volume of chaotic component of the phase space happens for certain values of the angular momentum. We conclude that a large fraction of regular trajectories in relation to all trajectories appears only when there is a possibility for the regular motion to perform a rotation different from that for a chaotic motion. When such difference is small, the regular motion disappears. The effective number of rotational modes can be used to estimate the difference in the type of rotation and is a convenient parameter which controls changes in the dynamics of the system.

MeSH terms

  • Computer Simulation*
  • Models, Molecular*
  • Motion
  • Protein Conformation
  • Proteins / chemistry*
  • Software

Substances

  • Proteins