Abstract
The objective of this paper is to outline a new approach to analyzing the geometry of macro-molecules and investigating important physical properties by means of simulations. The classical method of force field calculations requires minimizing the energy as a function of the Cartesian coordinates of all atoms. Due to the large number of variables this method is limited to relatively small molecules. We describe an approach to overcome this difficulty. On the one hand, the number of free variables is effectively reduced by assembling certain groups of atoms into configurational structures with considerably less degrees of freedom. In this way we build up a whole hierarchy of coordinate spaces with decreasing dimensions. On the other hand, approximations to the energy function with respect to these variables are constructed using methods from the theory of splines and radial basis functions. The hierarchical features of wavelet decompositions are utilized to exploit the physical importance of the different force field constants on the biological function of the macro-molecule.
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Butzlaff, M., Dahmen, W., Diekmann, S. et al. A hierarchical approach to force field calculations through spline approximations. J Math Chem 15, 77–92 (1994). https://doi.org/10.1007/BF01277550
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DOI: https://doi.org/10.1007/BF01277550