Annealed importance sampling of peptides

Edward Lyman, Daniel Zuckerman

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Annealed importance sampling assigns equilibrium weights to a nonequilibrium sample that was generated by a simulated annealing protocol [R. M. Neal, Stat. Comput. 11, 125 (2001)]. The weights may then be used to calculate equilibrium averages, and also serve as an "adiabatic signature" of the chosen cooling schedule. In this paper we demonstrate the method on the 50-atom dileucine peptide and an alanine 5-mer, showing that equilibrium distributions are attained for manageable cooling schedules. For dileucine, as naively implemented here, the method is modestly more efficient than constant temperature simulation. The alanine application demonstrates the success of the method when there is little overlap between the high (unfolded) and low (folded) temperature distributions. The method is worth considering whenever any simulated heating or cooling is performed (as is often done at the beginning of a simulation project or during a NMR structure calculation), as it is simple to implement and requires minimal additional computational expense. Furthermore, the naive implementation presented here can be improved.

Original languageEnglish (US)
Article number065101
JournalJournal of Chemical Physics
Volume127
Issue number6
DOIs
StatePublished - Aug 20 2007
Externally publishedYes

Fingerprint

Importance sampling
peptides
sampling
alanine
schedules
Cooling
cooling
Alanine
Peptides
simulated annealing
Simulated annealing
Temperature distribution
temperature distribution
simulation
signatures
Nuclear magnetic resonance
Heating
Atoms
nuclear magnetic resonance
heating

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Annealed importance sampling of peptides. / Lyman, Edward; Zuckerman, Daniel.

In: Journal of Chemical Physics, Vol. 127, No. 6, 065101, 20.08.2007.

Research output: Contribution to journalArticle

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