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. Author manuscript; available in PMC: 2014 Feb 5.
Published in final edited form as: J Phys Chem B. 2012 Aug 17;116(34):10145–10164. doi: 10.1021/jp3015047

FIG. 4.

FIG. 4

A pictorial representation of the asymptotic boundary conditions enforced in Model-2. The inner shell contains all atoms within a distance of 14Å from the active site iron center and is represented in cyan. This region is the most flexible part of the enzyme during Model-2 simulations. Atoms that are situated between 14Å and 16 Å from the iron center (represented in ochre) are constrained (see text) so as to allow the outer portion (greater that 16Å from the iron center and represented in grey) to remain frozen during dynamics.