Ensemble-based convergence analysis of biomolecular trajectories

Edward Lyman, Daniel Zuckerman

Research output: Contribution to journalArticle

77 Citations (Scopus)

Abstract

Assessing the convergence of a biomolecular simulation is an essential part of any careful computational investigation, because many fundamental aspects of molecular behavior depend on the relative populations of different conformers. Here we present a physically intuitive method to self-consistently assess the convergence of trajectories generated by molecular dynamics and related methods. Our approach reports directly and systematically on the structural diversity of a simulation trajectory. Straightforward clustering and classification steps are the key ingredients, allowing the approach to be trivially applied to systems of any size. Our initial study on met-enkephalin strongly suggests that even fairly long trajectories (∼50 ns) may not be converged for this small - but highly flexible - system.

Original languageEnglish (US)
Pages (from-to)164-172
Number of pages9
JournalBiophysical Journal
Volume91
Issue number1
DOIs
StatePublished - Jan 1 2006
Externally publishedYes

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Methionine Enkephalin
Molecular Dynamics Simulation
Cluster Analysis
Population

ASJC Scopus subject areas

  • Biophysics

Cite this

Ensemble-based convergence analysis of biomolecular trajectories. / Lyman, Edward; Zuckerman, Daniel.

In: Biophysical Journal, Vol. 91, No. 1, 01.01.2006, p. 164-172.

Research output: Contribution to journalArticle

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