Resolution exchange simulation.
We extend replica-exchange simulation in two ways and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution--i.e., between detailed and coarse-grained models. Such "resolution exchange" can be applied to molecular systems or spin systems. The second extension is to "pseudoexchange" simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduce the need for overlap between levels. Pseudoexchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
Edward
E
Lyman
F Marty
FM
Ytreberg
Daniel M
DM
Zuckerman
D000465:Algorithms; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*
D010455:Peptides; D011506:Proteins