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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/j.jcp.2011.12.022 , 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/j.jcp.2009.09.028, 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/j.jcp.2006.05.032,
2007.
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