Vol. 12, no.1, 2020


Description of molecule rotation in computer models of water using quaternions

Vladimir P. Voloshin, Yuri I. Naberukhin

Voevodsky Institute of Chemical Kinetics and Combustion SB RAS, http://www.kinetics.nsc.ru/
Novosibirsk 630090, Russian Federation
Е-mail: voloshin@kinetics.nsc.ru, naber@ngs.ru.

Received January 05, 2020; peer reviewed January 10, 2020; accepted January 15, 2020
Abstract. The motion of a rigid molecule in a computer model can be considered as the movement of its center of mass and rotation around an axis passing through this center. This article uses quaternion algebra to describe rotational motion. It provides an opportunity to study rotational motion almost as easily as translational, since the quaternion contains the axis and the angle of rotation in almost explicit form. We use this method to study the rotation of molecules in the molecular dynamics model of water. The distributions of angles between the translational displacement vectors and the axes of rotation of the molecules, as well as between these vectors and the internal vectors of the molecules (dipole moment, normal vector, and HH vector), are investigated. Correlations between the translational and rotational movements of the water molecule are established and the general character of its movement is determined. Appendix contains exact formulas and detailed descriptions of the procedures for using quaternions to describe the rotation of molecules.

Keywords: molecular dynamics simulation, water, translational displacement, angular displacement, correlation of displacement and rotation axis

PACS 45.20.dc, 47.11.-j.

RENSIT, 2020, 12(1):69-80. DOI: 10.17725/rensit.2020.12.069.

Full-text electronic version of this article - web site http://en.rensit.ru/vypuski/article/312/12(1)69-80e.pdf