Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, especially for the sampling of aqueous protein solutions in which there are large-scale solute conformation changes. Like the original REST (REST1), the new version (which we call REST2) also bypasses the poor scaling with system size of the standard Temperature Replica Exchange Method (TREM), reducing the number of replicas (parallel processes) from what must be used in TREM. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on…

• NS
  National Science Foundation
• NC
  National Centre for Supercomputing Applications
• NI
  National Institutes of Health