Abstract
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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1200-1202 |
| Number of pages | 3 |
| Journal | Journal of Chemical Theory and Computation |
| Volume | 2 |
| Issue number | 4 |
| DOIs | |
| State | Published - Dec 1 2006 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Computer Science Applications
- Physical and Theoretical Chemistry
Cite this
A second look at canonical sampling of biomolecules using replica exchange simulation. / Zuckerman, Daniel; Lyman, Edward.
In: Journal of Chemical Theory and Computation, Vol. 2, No. 4, 01.12.2006, p. 1200-1202.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A second look at canonical sampling of biomolecules using replica exchange simulation
AU - Zuckerman, Daniel
AU - Lyman, Edward
PY - 2006/12/1
Y1 - 2006/12/1
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.
UR - http://www.scopus.com/inward/record.url?scp=33750970357&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33750970357&partnerID=8YFLogxK
U2 - 10.1021/ct0600464
DO - 10.1021/ct0600464
M3 - Article
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 -