Ensemble-based convergence analysis of biomolecular trajectories

Biophys J. 2006 Jul 1;91(1):164-72. doi: 10.1529/biophysj.106.082941. Epub 2006 Apr 14.

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biopolymers / chemistry*
  • Computer Simulation
  • Elasticity
  • Models, Chemical*
  • Models, Molecular*
  • Motion
  • Multiprotein Complexes / chemistry*
  • Multiprotein Complexes / ultrastructure
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / ultrastructure
  • Stress, Mechanical

Substances

  • Biopolymers
  • Multiprotein Complexes
  • Proteins