MD simulation examples

Figure 4-19. SN2 reaction the changes in the selected interatomic distances (a) and angles along the IRC and the 300K MD simulation. Example geometries from the trajectory corresponding to the van der Waals complex are shown in panel c...

Discrete models treat individual atoms, molecules, or particles and can be deterministic or stochastic. Examples of the former include MD simulations. Examples of the latter are various MC methods, BD, DPD, DSMC, and LB simulations. There are different ensembles in which these simulations can be performed, depending on the quantities that one is interested in computing. 

Going beyond the mean-field level, several "hybrid" approaches are now being explored in MD simulations. Examples include a recent model [70] in which the immediate hydration of the solute is modeled explicitly by a layer of water molecules, and the GB model is used to treat the bulk continuum solvent outside the explicit simulation volume. A similar idea was recently found very effective in the context of replica-exchange simulations [71]. An explicit ion/implicit water (PB) solvation model for molecular dynamics of nucleic acids has recently been tested [72]. 

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