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LINCS: A linearconstraint solver formolecular simulations Berk HessHenk BekkerHerman J. C. Berendsen1997 год

LINCS: A linear constraint solver for molecular simulations
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Аннотация: In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1463–1472, 1997
Год издания: 1997
Авторы: Berk Hess, Henk Bekker, Herman J. C. Berendsen, J. G. E. M. Fraaije
Издательство: Wiley
Источник: Journal of Computational Chemistry
Ключевые слова: Protein Structure and Dynamics, Matrix Theory and Algorithms, Parallel Computing and Optimization Techniques