LINCS: A Linear Constraint Solver for molecular simulations

  • Hess B
  • Bekker H
  • Berendsen H
 et al. 
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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.

Author-supplied keywords

  • Constraints
  • Langevin dynamics
  • Molecular dynamics
  • SHAKE

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Authors

  • Berk Hess

  • Henk Bekker

  • Herman J.C. Berendsen

  • Johannes G.E.M. Fraaije

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