Parallel Replica

Parallel Replica#

Parallel Replica dynamics (PRD) is the simplest and the accurate way to accelerate a molecular dynamics simulation as discussed by Voter [PRD_Vot98] and more recently reviewed by Perez et al. [PRD_PUV15]. The only assumption made in this method is that the reactions satisfy first order kinetics.

\[\mathrm{Pr}(t) = k \exp (-k t)\]

PRD boosts the simulation linearly with the number of replicas and can be easily combined with other methods for extending the MD time scale, e.g. the hyperdynamics method, giving a multiplicative effect in the time scales that can be achieved.

In the PRD approach, \(N\) replicas of the system are made at first and then the momentum in each replica is randomized and dephasing stage is employed to decorrelate their motions. The simulation clock starts after this dephasing stage and stops when the first transition is detected in any of replicas. Because those \(N\) trajectories are independent, they can explore the phase space \(N\) times faster than using a single trajectory. The overall simulation clock is advanced by the sum of all the simulation times in replicas.

In order to work with distributed computing, we have modified the traditional scheme for running PRD. The replica generating and dephasing stage is exactly the same. However, we make all replicas run the same number of MD steps to avoid biasing the successful transition trajectories. In other words, results will only be reported back when the clients finish their full trajectories. The server increments the simulation time \(t\) until the first transition occurs.

In order to run Parallel Replica jobs:

  • Set job to parallel_replica in the [Main] section.

  • For regular MD the time step and length of the trajactory and parameters of thermostat can be set in the [Dynamics] section.

  • The temperature for the dynamics run is set in the [Main] section.

Configuration#

[Parallel Replica]

Changed in version 3.1_TBA: In TOML, this will be [Parallel_Replica]

References#

[PRD_PUV15]

Danny Perez, Blas P. Uberuaga, and Arthur F. Voter. The parallel replica dynamics method – Coming of age. Computational Materials Science, 100:90–103, April 2015. doi:10.1016/j.commatsci.2014.12.011.

[PRD_Vot98]

Arthur F. Voter. Parallel replica method for dynamics of infrequent events. Physical Review B, 57(22):R13985–R13988, June 1998. doi:10.1103/PhysRevB.57.R13985.

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