SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973–1977
Daniele Macuglia
Abstract
Abstract This essay traces the history of early molecular dynamics simulations, specifically exploring the development of SHAKE, a constraint-based technique devised in 1976 by Jean-Paul Ryckaert, Giovanni Ciccotti and the late Herman Berendsen at CECAM (Centre Européen de Calcul Atomique et Moléculaire). The work of the three scientists proved to be instrumental in giving impetus to the MD simulation of complex polymer systems and it currently underpins the work of thousands of researchers worldwide who are engaged in computational physics, chemistry and biology. Despite its impact and its role in bringing different scientific fields together, accurate historical studies on the birth of SHAKE are virtually absent. By collecting and elaborating on the accounts of Ryckaert and Ciccotti, this essay aims to fill this gap, while also commenting on the conceptual and computational difficulties faced by its developers.