The Scientific World Journal / 2013 / Article / Fig 1

Research Article

Common Force Field Thermodynamics of Cholesterol

Figure 1

Principal component analysis (PCA) regarding 250 structural snapshots of cholesterol sampled over 5 ns of molecular dynamics (MD) simulations using common force fields. (a) Nomenclature of 3 -hydroxy cholesterol (numbering restricted to carbon atoms). (b) PCA of bonds (from a total of 77). (c) PCA of angles (157 angles in total). (d) PCA of dihedrals (259 dihedrals all in all). Color-coded are the top-ranked 10% bonds/angles/dihedrals based on a selection of PCs recovering 90% of the original data set. Different colors represent different force fields and involve C–H bonds if applied to numbers.

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