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.

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  1. Banisch, Ralf; Hartmann, Carsten: A sparse Markov chain approximation of LQ-type stochastic control problems (2016)
  2. Xue, Xu; Yongjun, Wang; Zhihong, Li: Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation (2015)
  3. Escribano, Bruno; Akhmatskaya, Elena; Mujika, Jon I.: Combining stochastic and deterministic approaches within high efficiency molecular simulations (2013)
  4. Fackeldey, Konstantin; Bujotzek, Alexander; Weber, Marcus: A meshless discretization method for Markov state models applied to explicit water peptide folding simulations (2013)
  5. Martins do Canto, A.M.T.; Carvalho, A.J.Palace; Ramalho, J.P.Prates; Loura, Luís M.S.: Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interaction (2012)
  6. Liu, Bin; Wang, Jizeng; Fan, Xiaojun; Kong, Yong; Gao, Huajian: An effective bead-spring model for polymer simulation (2008)
  7. Berendsen, Herman J. C.: Simulating the physical world. Hierarchical modeling from quantum mechanics to fluid dynamics. (2007)
  8. Gonnet, Pedro: P-SHAKE: a quadratically convergent SHAKE in $O(n^2)$ (2007)
  9. Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko: Long-range interactions and parallel scalability in molecular simulations (2007)
  10. Zuo, Zhili; Gang, Chen; Zou, Hanjun; Mok, Puah Chum; Zhu, Weiliang; Chen, Kaixian; Jiang, Hualiang: Why does $\beta $-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies (2007)
  11. Lee, Sang-Ho; Palmo, Kim; Krimm, Samuel: WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates (2005)
  12. Yoneya, Makoto: A generalized non-iterative matrix method for constraint molecular dynamics simulations (2001)