title: How hot? Systematic convergence of the replica exchange method using multiple reservoirs.
abstract: We have devised a systematic approach to converge a replica exchange molecular dynamics simulation by dividing the full temperature range into a series of higher temperature reservoirs and a finite number of lower temperature subreplicas. A defined highest temperature reservoir of equilibrium conformations is used to help converge a lower but still hot temperature subreplica, which in turn serves as the high-temperature reservoir for the next set of lower temperature subreplicas. The process is continued until an optimal temperature reservoir is reached to converge the simulation at the target temperature. This gradual convergence of subreplicas allows for better and faster convergence at the temperature of interest and all intermediate temperatures for thermodynamic analysis, as well as optimizing the use of multiple processors. We illustrate the overall effectiveness of our multiple reservoir replica exchange strategy by comparing sampling and computational efficiency with respect to replica exchange, as well as comparing methods when converging the structural ensemble of the disordered Abeta(21-30) peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values.
authors: Department of Bioengineering, University of California, Berkeley, California, USA.
authors: Jory Z
authors: JZ
authors: Ruscio
authors: Nicolas L
authors: NL
authors: Fawzi
authors: Teresa
authors: T
authors: Head-Gordon
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry*; D004735:Energy Transfer; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000737:chemistry*; D013057:Spectrum Analysis; D013696:Temperature; D014867:Water / Q000737:chemistry
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; C501831:amyloid beta-protein (21-30); D014867:Water