An optimized replica exchange molecular dynamics method

摘要

We introduce a new way to perform swaps between replicas in replica exchange moleculardynamics simulations. The method is based on a generalized canonical probability distributionfunction and flattens the potential of mean force along the temperature coordinate, such that arandom walk in temperature space is achieved. Application to a Go model of protein A showed thatthe method is more efficient than conventional replica exchange. The method results in a constantprobability distribution of the replicas over the thermostats, yields a minimum round-trip timebetween extremum temperatures, and leads to faster ergodic convergence.