Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Efficiency of Rotational Operators for Geometric Manipulation of Chain Molecules

  • Seok, Chaok (Department of Chemistry, College of Natural Sciences, Seoul National University) ;
  • Coutsias, Evangelos A. (Department of Mathematics and Statistics, University of New Mexico)
  • Published : 2007.10.20
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Abstract

Geometric manipulation of molecules is an essential elementary component in computational modeling programs for molecular structure, stability, dynamics, and design. The computational complexity of transformation of internal coordinates to Cartesian coordinates was discussed before.1 The use of rotation matrices was found to be slightly more efficient than that of quaternion although quaternion operators have been widely advertised for rotational operations, especially in molecular dynamics simulations of liquids where the orientation is a dynamical variable.2 The discussion on computational efficiency is extended here to a more general case in which bond angles and sidechain torsion angles are allowed to vary. The algorithm of Thompson3 is derived again in terms of quaternions as well as rotation matrices, and an algorithm with optimal efficiency is described. The algorithm based on rotation matrices is again found to be slightly more efficient than that based on quaternions.

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References

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  3. Polymer conformations in internal (polyspherical) coordinates pp.1096987X, 2010, https://doi.org/10.1002/jcc.21474
  4. Physical Chemistry Research Articles Published in the Bulletin of the Korean Chemical Society: 2003-2007 vol.29, pp.2, 2008, https://doi.org/10.5012/bkcs.2008.29.2.450