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 language | English (US) |
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Pages (from-to) | 164-172 |
Number of pages | 9 |
Journal | Biophysical Journal |
Volume | 91 |
Issue number | 1 |
DOIs | |
State | Published - 2006 |
Externally published | Yes |
ASJC Scopus subject areas
- Biophysics