LINCS: A linear constraint solver for molecular simulations

Journal of Computational ChemistryVolume 18, Issue 12 p. 1463-1472 LINCS: A linear constraint solver for molecular simulations Berk Hess, Berk Hess Bioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsSearch for more papers by this authorHenk Bekker, Henk Bekker Department of Computer Science, University of Groningen, Groningen, The NetherlandsSearch for more papers by this authorHerman J. C. Berendsen, Herman J. C. Berendsen Bioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsSearch for more papers by this authorJohannes G. E. M. Fraaije, Corresponding Author Johannes G. E. M. Fraaije Bioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsBioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsSearch for more papers by this author Berk Hess, Berk Hess Bioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsSearch for more papers by this authorHenk Bekker, Henk Bekker Department of Computer Science, University of Groningen, Groningen, The NetherlandsSearch for more papers by this authorHerman J. C. Berendsen, Herman J. C. Berendsen Bioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsSearch for more papers by this authorJohannes G. E. M. Fraaije, Corresponding Author Johannes G. E. M. Fraaije Bioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsBioson Research Institute, Lab of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The NetherlandsSearch for more papers by this author First published: 07 December 1998 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-HCitations: 4,360AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL 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 Citing Literature Volume18, Issue12September 1997Pages 1463-1472 RelatedInformation