Parallel replica dynamics exchange

In the parallel replica dynamics method the time scale of MD simulations is extended by distributing the computation on many processors in a way that requires only tittle information exchange between them yielding almost linear speed-up in many cases. This method is applicable whenever the distribution of escape times t from a potential (or free) energy basin is exponential, ... 

Molecular dynamics has also been used to replace the MC moves for conformational advancement [43]. In the molecular dynamics version of parallel tempering, often referred to as replica exchange molecular dynamics, momenta are used in the propagation scheme such that a constant temperature is maintained between the swaps. After the swap in conformational space (with the same acceptance criterion as in the MC implementation), a readjustment in momentum space is also needed. This is done by renewing the momenta for replica i by the transformation... 

One increasingly popular method which lead to non-dynamical trajectories is replica-exchange MC or MD [11-13], which employs parallel simulations at a ladder of temperatures. The "trajectory" at any given temperature includes repeated visits from a number of (physically continuous) trajectories wandering in temperature space. Because the continuous trajectories are correlated in the usual sequential way, their intermittent — that is, non-sequential — visits to the various specific temperatures produce non-sequential correlations when one of those temperatures is considered as a separate ensemble or "trajectory" [14]. Less prominent examples of non-dynamical simulations occur in a broad class of polymer-growth algorithms (e.g., refs. 15-17). 

Two-way parallel interfaces. These involve a two-way dynamic transfer of information between two simulations running in parallel at two different modelling levels. An example includes running both an MM and CG simulation of a system and using replica exchange ° moves to exchange coordinates between the two levels. 

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