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Biophys J. 2006 Jul 1;91(1):164-72. Epub 2006 Apr 14.

Ensemble-based convergence analysis of biomolecular trajectories.

Author information

1
Department of Computational Biology, School of Medicine, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

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 (approximately 50 ns) may not be converged for this small--but highly flexible--system.

PMID:
16617086
PMCID:
PMC1479051
DOI:
10.1529/biophysj.106.082941
[Indexed for MEDLINE]
Free PMC Article

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