LINCS swMATH ID: 8880 Software Authors: Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E.M Description: LINCS: a linear constraint solver for molecular simulations. In this chapter 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 3 to 4 times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. Homepage: http://www.cs.rug.nl/~bekker/publications/lincs.pdf Related Software: Gromacs; SETTLE; VMD; PROCHECK; P-LINCS; CHARMM; Q-SiteFinder; PyMOL; AutoDock Vina; SWISS-MODEL; I-TASSER; GROMOS; Matlab; DL_POLY; Octave; ZIBAmira; ZIBgridfree; Amira; GSHMC; MMM2D Cited in: 22 Documents all top 5 Cited by 71 Authors 2 Baker, Nathan A. 2 Lei, Huan 1 Akhmatskaya, Elena 1 Banisch, Ralf 1 Baz, Jörg 1 Berendsen, Herman J. C. 1 Bu, Bing 1 Bujotzek, Alexander 1 Carvalho, A. J. Palace 1 Chen, Kaixian 1 Cruz-Chú, Eduardo R. 1 Desbrun, Mathieu 1 Diao, Jiajie 1 Escribano, Bruno 1 Fackeldey, Konstantin 1 Fan, Xiaojun 1 Gang, Chen 1 Gao, Huajian 1 Gao, Peiyuan 1 Gonnet, Pedro 1 Grogan, Francesca 1 Hartmann, Carsten 1 Heider, Yousef 1 Hernandez Padilla, Carlos Alberto 1 Hopp-Hirschler, Manuel 1 Jamdar, Virashree 1 Ji, Baohua 1 Jiang, Hualiang 1 Kong, Yong 1 Krimm, Samuel 1 Kumari, Sweta 1 Lee, Sangho 1 Leimkuhler, Benedict J. 1 Li, Dechang 1 Li, Jing 1 Li, Xiantao 1 Liu, Bin 1 Loura, Luís M. S. 1 Lu, Lanyuan 1 Lulu, Sajitha 1 Mahapatra, Rajani Kanta 1 Markert, Bernd 1 Martins do Canto, A. M. T. 1 Matthews, Charles E. 1 Michels, Dominik Ludewig 1 Mohana Priya, Arumugam 1 Mok, Puah Chum 1 Mol, Milsee 1 Mujika, Jon I. 1 Nieken, Ulrich 1 Palmo, Kim 1 Patil, Sandeep P. 1 Ramalho, J. P. Prates 1 Rout, Subhashree 1 Shen, Zuowei 1 Shinde, Sonali 1 Singh, Shailza 1 Stinis, Panagiotis 1 Tauqueer, Mohammad 1 Tong, Dudu 1 Wang, Jizeng 1 Weber, Marcus 1 Xue, Xu 1 Yang, Jianbin 1 Yoneya, Makoto 1 Yongjun, Wang 1 Zhihong, Li 1 Zhu, Guanhua 1 Zhu, Weiliang 1 Zou, Hanjun 1 Zuo, Zhili all top 5 Cited in 10 Serials 7 Journal of Computational Physics 4 Journal of Theoretical Biology 2 Computer Methods in Applied Mechanics and Engineering 1 Computers and Fluids 1 Central European Journal of Mathematics 1 Computational Biology and Chemistry 1 Interdisciplinary Applied Mathematics 1 Acta Mechanica Sinica 1 Computational & Mathematical Methods in Medicine 1 Mathematical Control and Related Fields all top 5 Cited in 16 Fields 9 Biology and other natural sciences (92-XX) 7 Statistical mechanics, structure of matter (82-XX) 6 Numerical analysis (65-XX) 3 Probability theory and stochastic processes (60-XX) 3 Fluid mechanics (76-XX) 3 Quantum theory (81-XX) 2 Computer science (68-XX) 1 General and overarching topics; collections (00-XX) 1 Dynamical systems and ergodic theory (37-XX) 1 Calculus of variations and optimal control; optimization (49-XX) 1 Statistics (62-XX) 1 Mechanics of deformable solids (74-XX) 1 Optics, electromagnetic theory (78-XX) 1 Classical thermodynamics, heat transfer (80-XX) 1 Operations research, mathematical programming (90-XX) 1 Systems theory; control (93-XX) Citations by Year