Fast Calculation of the Relaxation Matrix

  • Mark J. Forster
Part of the NATO ASI Series book series (NSSA, volume 225)


The relaxation matrix for a macromolecule is a 2D array holding the set of auto and cross relaxation rates. This is used in the numerical simulation of NOEs for given candidate structures. Structure refinement routines that compare experimental and simulated NOEs require many recalculations of the matrix and algorithm efficiency should be an important consideration. Three algorithms are described and their relative efficiencies compared by computing relaxation matrices for model macromolecules. An interaction distance cutoff of 8 Angstroms greatly reduces the calculation time for large systems and introduces only a small truncation error. Further performance improvements, at the same level of accuracy, were obtained by using a 3D array/linked list data structure to avoid calculating the full set of N(N — 1)/2 distances.


Distance Cutoff Spectral Density Function Nuclear Overhauser Effect Relaxation Matrix Cross Relaxation Rate 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer Science+Business Media New York 1991

Authors and Affiliations

  • Mark J. Forster
    • 1
  1. 1.National Institute for Biological Standards and ControlHertfordshireUK

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