Journal
BIOPHYSICAL JOURNAL
Volume 91, Issue 1, Pages 164-172Publisher
CELL PRESS
DOI: 10.1529/biophysj.106.082941
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Funding
- NIEHS NIH HHS [T32 ES007318, ES007318] Funding Source: Medline
- NIGMS NIH HHS [GM070987, R01 GM070987] Funding Source: Medline
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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 (similar to 50 ns) may not be converged for this small - but highly flexible - system.
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