SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973–1977

Author:

Macuglia Daniele

Abstract

AbstractThis 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.

Publisher

Springer Science and Business Media LLC

Subject

History and Philosophy of Science,Mathematics (miscellaneous)

Reference84 articles.

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2. Alder, Berni J., and Thomas E. Wainwright. 1958. Molecular dynamics by electronic computers. In Proceedings of the international symposium on transport processes in statistical mechanics, held in Brussels, August 27–31, 1956, ed. Ilya Prigogine, 97–131. New York: Interscience Publisher.

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5. Barker, John A., and Douglas Henderson. 1967a. Perturbation theory and equation of state for fluids: The square-well potential. The Journal of Chemical Physics 47 (8): 2856–2861.

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