Newtonian molecular dynamics in general curvilinear internal coordinates

• Published in: Chemical physics letters Vol. 353; no. 5; pp. 400 - 406
• Main Authors: Pulay, P., Paizs, B.
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier B.V 26-02-2002; Elsevier Science
• Subjects: Atomic and molecular physics; Calculations and mathematical techniques in atomic and molecular physics (excluding electron correlation calculations); Electronic structure of atoms, molecules and their ions: theory; Exact sciences and technology; Molecular dynamics and other numerical methods; Physics; Molecules; Conformational dynamics; Digital simulation; Cyclohexane; Molecular dynamics method; Internal coordinate; Organic compounds
• ISSN: 0009-2614; 1873-4448
• DOI: 10.1016/S0009-2614(02)00051-9

A simple formulation of Newtonian molecular dynamics in general internal coordinates is given. Our equation for the internal acceleration does not require the transformation matrix from internal to Cartesian coordinates, only the much simpler first and second-order transformation from Cartesians to internals. The formulation has a simple, common general expression for the centrifugal/Coriolis contribution to the internal acceleration. The method has been implemented using natural internal coordinates, and can be easily applied to cyclic molecules. Applications for the internal dynamics of cyclohexane are shown.