A second look at canonical sampling of biomolecules using replica exchange simulation

Daniel Zuckerman, Edward Lyman

Research output: Contribution to journalArticle

74 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)1200-1202
Number of pages3
JournalJournal of Chemical Theory and Computation
Volume2
Issue number4
DOIs
StatePublished - Dec 1 2006
Externally publishedYes

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Biomolecules
replicas
sampling
Sampling
Tempering
Peptides
tempering
simulation
Atoms
Temperature
peptides
atoms
temperature

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 journalArticle

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