Resolution exchange simulation with incremental coarsening

Edward Lyman, Daniel Zuckerman

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

We previously developed an algorithm, called "resolution exchange", which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations. Here, we demonstrate a generally applicable incremental coarsening procedure and apply the algorithm to a larger peptide, met-enkephalin. In addition, we demonstrate a combination of resolution and temperature exchange, in which the coarser simulations are also at elevated temperatures. Both simulations are implemented in a "top-down" mode, to allow efficient allocation of CPU time among the different replicas.

Original languageEnglish (US)
Pages (from-to)656-666
Number of pages11
JournalJournal of Chemical Theory and Computation
Volume2
Issue number3
DOIs
StatePublished - Dec 1 2006
Externally publishedYes

Fingerprint

Coarsening
Methionine Enkephalin
Peptides
Program processors
Conformations
simulation
Sampling
Temperature
replicas
peptides
sampling
temperature
high resolution

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

Cite this

Resolution exchange simulation with incremental coarsening. / Lyman, Edward; Zuckerman, Daniel.

In: Journal of Chemical Theory and Computation, Vol. 2, No. 3, 01.12.2006, p. 656-666.

Research output: Contribution to journalArticle

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