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The following publications describe some of the more important novel algorithms implemented in mdcore:

  • P. Gonnet, A Short Note on the Fast Evaluation of Dihedral Angle Potentials and their Derivatives, Journal of Computational Physics, in Press, doi:10.1016/ , 2012.

  • P. Gonnet, Pairwise Verlet lists: combining cell lists and Verlet lists to improve memory locality and parallelism, Journal of Computational Chemistry, 33(1):76-81, doi: 10.1002/jcc.21945, 2012.

  • P. Gonnet, Efficient algorithms for molecular dynamics simulations on the Cell Broadband Engine Architecture, ICNAAM 2010: International Conference of Numerical Analysis and Applied Mathematics 2010, Rhodes, AIP Conf. Proc. 1281:1305-1308, doi:10.1063/1.3497953, 2010.

  • P. Gonnet, Using piecewise polynomials for faster potential function evaluation, Journal of Computational Physics, 229(2):313-324, doi:10.1016/, 2010.

  • P. Gonnet, A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations, Journal of Computational Chemistry, 28(2):570-573, doi:10.1002/jcc.20563, 2007.

  • P. Gonnet, P-SHAKE: A quadratically convergent SHAKE in O(n(2)), Journal of Computational Physics, 220(2):740-750, doi:10.1016/, 2007.