Work

Resolution Exchange Simulation

Year: 2006

Type: article

Abstract: 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.

Source: Physical Review Letters

DOI: 10.1103/physrevlett.96.028105

Authors: Edward Lyman, F. Marty Ytreberg, Daniel M. Zuckerman

Institution: University of Pittsburgh

Language: English

Topic: Advanced Physical and Chemical Molecular Interactions

Subfield: Physical and Theoretical Chemistry

Field: Chemistry

Domain: Physical Sciences

Open Access status: green

Funders: National Institute of General Medical Sciences, National Institute of Environmental Health Sciences

Awards: G2249132229, G2506435269, G5231225057, G6513208