Temperature accelerated dynamics

Temperature accelerated dynamics runs a hot trajectory at [Main] temperature. The client job is tad. The cold temperature is [TAD] low_temperature, default 300 K. min_prefactor (default 0.001) and confidence (default 0.001) set how long that hot trajectory continues after a transition. The trajectory length and the step come from [Dynamics]. When thermostat is omitted, the client uses andersen. The trajectory tests for a new state on the parallel-replica state-check interval. The record interval in that section can refine the crossing.

A barrier Eb on the trajectory scales the hot transition time by exp(Eb/kB * (1/low_temperature - 1/temperature)). tmin is the shortest corrected time. factor is ln(1/confidence) / min_prefactor. The hot trajectory can stop before [Dynamics] time. It stops once the hot clock passes factor * (tmin / factor) raised to low_temperature / temperature.

[Main]
job = tad
temperature = 600

[TAD]
low_temperature = 300
min_prefactor = 0.001
confidence = 0.001

[Dynamics]
time_step = 1.0
time = 1000.0