Resolution exchange simulation

Edward Lyman, F. Marty Ytreberg, Daniel Zuckerman

Research output: Contribution to journalArticle

149 Citations (Scopus)

Abstract

We extend replica-exchange simulation in two ways and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution-i.e., between detailed and coarse-grained models. Such "resolution exchange" can be applied to molecular systems or spin systems. The second extension is to "pseudoexchange" simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduce the need for overlap between levels. Pseudoexchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.

Original languageEnglish (US)
Article number028105
JournalPhysical Review Letters
Volume96
Issue number2
DOIs
StatePublished - Jan 20 2006
Externally publishedYes

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replicas
simulation
ladders
peptides
atoms

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Resolution exchange simulation. / Lyman, Edward; Ytreberg, F. Marty; Zuckerman, Daniel.

In: Physical Review Letters, Vol. 96, No. 2, 028105, 20.01.2006.

Research output: Contribution to journalArticle

Lyman, Edward ; Ytreberg, F. Marty ; Zuckerman, Daniel. / Resolution exchange simulation. In: Physical Review Letters. 2006 ; Vol. 96, No. 2.
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