Orientational dynamics energy landscapes

Intuitively, D appears to be well-placed to capture the dynamical signature of the coupling between orientational and translational order. In the energy landscape formalism the time-dependent position rft) of a particle i can be resolved into two components rft) = Rft) + Sft), where Rft) is the spatial position of the particle i in the inherent structure for the basin inhabited at time and S ft) is the intrabasin displacement away from that inherent structure [159], It has been theoretically argued that the replacement of the real positions r (f) by the corresponding inherent structure positions in the Einstein relation yields an equivalent diffusion description [159, 160]. Such a proposition, which has been verified in simulations [159, 160], forms the foundation of the analysis presented here. 

We describe interatomic interactions using the functional form U q) dehned by the CHARMM 27 force field, a standard force field available in many biomolecular-oriented molecular dynamics codes. For the sake of simplicity, all the simulations are carried out in vacuum as the free-energy landscape in such conditions presents several interesting features and has been studied previously using many different free-energy methods (see, e.g.. Refs. 30-35) thus being a perfect test bed for the discussion. 

---