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A short note on the fast evaluation of dihedral angle potentials and their derivatives. (English) Zbl 1245.82002

Summary: Dihedral angle potentials, which are used in many force fields for molecular dynamics simulations, model the energy of twisting a bond as a function of the angle between surfaces spanned by particles.

MSC:

82-08 Computational methods (statistical mechanics) (MSC2010)

Software:

NAMD; Gromacs; DESMOND

References:

[1] Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P., A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, Journal of Computational Chemistry, 24, 16, 1999-2012 (2003)
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[6] Allured, V. S.; Kelly, C. M.; Landis, C. R., SHAPES empirical force field: new treatment of angular potentials and its application to square-planar transition-metal complexes, Journal of the American Chemical Society, 113, 1, 1-12 (1991)
[7] Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M., UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations, Journal of the American Chemical Society, 114, 25, 10024-10035 (1992)
[8] K. Bowers, E. Chow, H. Xu, R. Dror, M. Eastwood, B. Gregersen, J. Klepeis, I. Kolossvary, M. Moraes, F. Sacerdoti, J. Salmon, Y. Shan, D. Shaw, Scalable algorithms for molecular dynamics simulations on commodity clusters, in: Proceedings of the ACM/IEEE SC 2006 Conference, 2006, p. 43. doi:10.1109/SC.2006.54; K. Bowers, E. Chow, H. Xu, R. Dror, M. Eastwood, B. Gregersen, J. Klepeis, I. Kolossvary, M. Moraes, F. Sacerdoti, J. Salmon, Y. Shan, D. Shaw, Scalable algorithms for molecular dynamics simulations on commodity clusters, in: Proceedings of the ACM/IEEE SC 2006 Conference, 2006, p. 43. doi:10.1109/SC.2006.54
[9] Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kal, L.; Schulten, K., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, 26, 16, 1781-1802 (2005)
[10] Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E., GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, Journal of Chemical Theory and Computation, 4, 3, 435-447 (2008)
[11] Clenshaw, C. W., A note on the summation of Chebyshev series, Mathematical Tables and Other Aids to Computation, 9, 51, 118-120 (1955) · Zbl 0065.05403
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