Abstract
Reducing the cost of the nonbonded energy and force computations is of primary importance in molecular mechanics and dynamics simulations of biomolecules. This is because the direct evaluation of these nonbonded interactions involving all atom pairs has the complexity of O(N 2) where N is the number of atoms. Recall that the bonded terms are local and thus have a linear computational complexity; see homework assignment 8 for a related exercise.
Hofstadter’s law: It always takes longer than you expect, ven when you take into account Hofstadter’s law.
Douglas R. Hofstadter, in Godel, Escher, Bach, 1979 (1945—).
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© 2002 Springer Science+Business Media New York
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Schlick, T. (2002). Nonbonded Computations. In: Molecular Modeling and Simulation. Interdisciplinary Applied Mathematics, vol 21. Springer, New York, NY. https://doi.org/10.1007/978-0-387-22464-0_9
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DOI: https://doi.org/10.1007/978-0-387-22464-0_9
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