Cycloalkanes Directory Reference Detailed DescriptionThe cycloalkanes are molecules that include loops of carbon atoms. The presence of a loop constraint makes CuikSuite specially adequate tool to analyze their conformational space. Note that the formulation we use here for the cycloalkanes is not based on distances (as we did in our JCC paper), but on vectors and rotation matrices, as in our more recent TRO paper. Moreover, note that in the formulation of the cycloalkanes, we use a variant of the formulation described in our recent TRO paper. We do not use orthonormal reference frames for the links but we use the two vectors aligned with the rotation axis coincident in each carbon to defined a non-orthogonal reference frame. This produces equation sets that can be easily simplified avoiding numerical issues. Please, check the individual files for details on these experiments: References
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