Skip to main content
. 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. 2.

FIG. 2

The two active site model systems used for the AIMD simulation of rare events. (i) Model-1 contains 50 atoms and is similar to that used in Refs. 7,9. (ii) Model-2 is treated using a QM/MM description. (See supporting information (S. I.) for a discussion on the asymptotic boundary conditions used to obtain the dynamical subset of 2174 atoms shown here.) The color codes for the QM region (shown using a CPK representation) are: carbon (cyan), hydrogen (white), oxygen (red), nitrogen (blue), iron (green) and the transferring pro-S hydrogen is represented in yellow. The remaining atoms shown in Figure (ii), using a line representation, are treated at the MM level.