title: Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding.
abstract: Temperature-based replica exchange (T-ReX) enhances sampling of molecular dynamics simulations by autonomously heating and cooling simulation clients via a Metropolis exchange criterion. A pathological case for T-ReX can occur when a change in state (e.g., folding to unfolding of a protein) has a large energetic difference over a short temperature interval leading to insufficient exchanges amongst replica clients near the transition temperature. One solution is to allow the temperature set to dynamically adapt in the temperature space, thereby enriching the population of clients near the transition temperature. In this work, we evaluated two approaches for adapting the temperature set: a method that equalizes exchange rates over all neighbor temperature pairs and a method that attempts to induce clients to visit all temperatures (dubbed "current maximization") by positioning many clients at or near the transition temperature. As a test case, we simulated the 57-residue SH3 domain of alpha-spectrin. Exchange rate equalization yielded the same unfolding-folding transition temperature as fixed-temperature ReX with much smoother convergence of this value. Surprisingly, the current maximization method yielded a significantly lower transition temperature, in close agreement with experimental observation, likely due to more extensive sampling of the transition state.
authors: U S Army Research Laboratory, Computational Sciences and Engineering Branch, Aberdeen Proving Ground, Maryland 21005, USA. michael.scott.lee@us.army.mil
authors: Michael S
authors: MS
authors: Lee
authors: Mark A
authors: MA
authors: Olson
mesh_terms: D044367:Phase Transition; D017510:Protein Folding; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry*; D013696:Temperature
chemical_list: D011506:Proteins