Sampling, multiple molecular dynamics

In such cases, the MEHMC method could be employed in combination with an enhanced sampling method that deforms the effective energy surface (but preserves the location of the potential minima), such as that in [29, 97]. Likewise, it may be worthwhile to explore the use of a reversible multiple-time-scale molecular dynamics propagator [103] with MEHMC to accelerate the dynamical propagation. 

The picosecond internal dynamics of myoglobin was explored by measuring inelastic neutron scattering by Smith et al. [25]. At low temperatures they found the dynamics to be harmonic while at higher temperatures a considerable quasielastic scattering was detected. Agreement between the experimentally observed spectra and that calculated from molecular dynamics simulations also showed evidence for restriction of the conformational space sampled at 80 K relative to 300 K. On the basis of these results it was concluded that the protein is trapped in local minima at low temperatures in accord with the multiple substate model suggested by low temperature flash photolysis experiments and previous molecular dynamics simulations. Comparison of atomic fluctuation data sets collected at both 325 K and 80 K confirms that the room temperature... 

Proctor et al. evaluated multiple docking poses by the stability of the pose during a subsequent simulation [126]. They used non-classical discrete molecular dynamics simulations which provide a fast sampling based on multiple independent... 

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