Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude

Local Resampling Trick for Focused Molecular Dynamics

We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can lead to incorrect sampling if the selection depends on the configuration in a way that is not accounted for. We avoid this pitfall by introducing appropriate auxiliary variables. This results in an implementation that is closely related to "configurational freezing" and "elastic barrier dynamical freezing." We implement the method and validate that it can be used to supplement conventional molecular dynamics in free energy calculations (absolute hydration and relative binding).