"Efficiency reduction and pseudo-convergence in replica exchange sampling of peptide folding-unfolding equilibria"Robert Denschlag, Martin Lingenheil, and Paul Tavan
Chem. Phys. Lett. 458, 244-248 (2008)
Replica exchange (RE) molecular dynamics (MD) simulations are frequently applied to sample the folding-unfolding equilibria of β-hairpin peptides in solution, because efficiency gains are
expected from this technique. Using a three-state Markov model featuring key aspects of β-hairpin folding we show that RE simulations can be less efficient than conventional techniques. Furthermore we demonstrate that one is easily seduced to erroneously assign convergence to the RE sampling, because RE ensembles can
rapidly reach long-lived stationary states. We conclude that typical REMD simulations covering a few tens of nanoseconds are by far too short for sufficient sampling of β-hairpin folding-unfolding equilibria.
BMO authors (in alphabetic order):
Photoswitchable model peptides and their conformational dynamics