Parallel replica dynamics

Keywords infrequent events transition-state theory accelerated dynamics hyperdynamics parallel-replica dynamics temperature-accelerated dynamics molecular dynamics bond-boost hyperdynamics parallel-accelerated dynamics Cu(100)... 

Figure 4 Left Distribution of hopping times for an adatom at a solid-liquid interface at 600 K for conventional molecular dynamics and for superstate parallel-replica dynamics. Right Temperature dependence of the hopping rate for an adatom at a dry interface and at a wet interface as obtained using superstate parallel-replica dynamics.

Uberuaga, B.P., Stuart, S.J., Voter, A.F. Parallel replica dynamics for driven systems derivation and application to strained nanotubes. Phys. Rev. B 2007, 75, 014301-1-9. 

Panel d illustrates parallel replica dynamics (PRD). First, a system A is replicated on a large number p of processors running in parallel (here, p=4). Ater randomization of momenta and equilibration, the dynamics of all p uncorrelated replicas are monitored at the same temperature. The simulation clock stops when the first transition of interest is detected in any of replicas. After that, the simulation clock is advanced by the accumulated trajectory time summed over all replicas, the detected configuration (B) is replicated on all processors, and the whole process is restarted. 

For systems in which the dynamics consist of long stays in the basins around potential energy minima interrupted by swift hops between them passing through saddle points, the assumptions of TST are often obeyed and the long time dynamics can be studied with the accelerated MD methods [20] discussed in Sect. 4. hi these approaches, which include parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics, the rate of esct ie from the minima is artificially enhanced in one way or another. The natural dynamics on long time scales is then reconstructed from such boosted simulations and often dramatic speed-ups can be achieved. 

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, ... 

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