TY - JOUR
T1 - A second look at canonical sampling of biomolecules using replica exchange simulation
AU - Zuckerman, Daniel M.
AU - Lyman, Edward
N1 - Copyright:
Copyright 2007 Elsevier B.V., All rights reserved.
PY - 2006
Y1 - 2006
N2 - The replica exchange approach, also called parallel tempering, is gaining popularity for biomolecular simulation. We ask whether the approach is likely to be efficient compared to standard simulation methods for fixed-temperature equilibrium sampling. To examine the issue, we make a number of straightforward observations on how "fast" high-temperature molecular simulations can be expected to run, as well as on how to characterize efficiency in replica exchange. Although our conclusions remain to be fully established, on the basis of a range of results in the literature and some of our own work with a 50-atom peptide, we are not optimistic for the efficiency of replica exchange for the canonical sampling of biomolecules.
AB - The replica exchange approach, also called parallel tempering, is gaining popularity for biomolecular simulation. We ask whether the approach is likely to be efficient compared to standard simulation methods for fixed-temperature equilibrium sampling. To examine the issue, we make a number of straightforward observations on how "fast" high-temperature molecular simulations can be expected to run, as well as on how to characterize efficiency in replica exchange. Although our conclusions remain to be fully established, on the basis of a range of results in the literature and some of our own work with a 50-atom peptide, we are not optimistic for the efficiency of replica exchange for the canonical sampling of biomolecules.
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U2 - 10.1021/ct0600464
DO - 10.1021/ct0600464
M3 - Article
AN - SCOPUS:33750970357
VL - 2
SP - 1200
EP - 1202
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
SN - 1549-9618
IS - 4
ER -