Paper Info
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 A beta(21-30) peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 31: 620-627, 2010
Year
DOI
Venue
2010
10.1002/jcc.21355
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
replica exchange,bimolecular simulation,NMR,enhanced sampling
Convergence (routing),Statistical physics,Replica,Nuclear Overhauser effect,Finite set,Hot Temperature,Atmospheric temperature range,Computational chemistry,Chemistry,Molecular dynamics,Sampling (statistics)
Journal
Volume
Issue
ISSN
31
3
0192-8651
Citations 
PageRank 
References 
0
0.34
2
Authors
3
Name
Order
Citations
PageRank
Jory Z. Ruscio110.78
Nicolas L. Fawzi200.34
Teresa Head-Gordon3276.25