Paper Citing NAMD - Abstract
Lyman, Edward; Zuckerman, Daniel M.
Ensemble-based convergence analysis of biomolecular trajectories
BIOPHYSICAL JOURNAL, 91:164-172, JUL 2006
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.
