LINCS: A linear constraint solver for molecular simulations
Berk HessBioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsHenk BekkerDepartment of Computer Science, University of Groningen, Groningen, The NetherlandsHerman J. C. BerendsenBioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsJ. G. E. M. FraaijeBioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
1997en
ABI
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
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