LINCS: A linear constraint solver for molecular simulations
B Hess, H Bekker, HJC Berendsen… - Journal of …, 1997 - Wiley Online Library
B Hess, H Bekker, HJC Berendsen, JGEM Fraaije
Journal of computational chemistry, 1997•Wiley Online LibraryIn 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 …
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 …
Abstract
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
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