Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency

A. Amadei, G. Chillemi, M. A. Ceruso, A. Grottesi, and A. Di Nola
Department of Chemistry, University of Rome "La Sapienza," P.le A. Moro 5, 00185, Rome, Italy

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Abstract

From a specific definition of the roto-translational (external) and intramolecular (internal) coordinates, a constrained dynamics algorithm is derived for removing the roto-translational motions during molecular dynamics simulations, within the leap-frog integration scheme. In the paper the theoretical basis of this new method and its statistical mechanical consistency are reported, together with two applications.