Resolution exchange simulation with incremental coarsening

Edward Lyman; Daniel M. Zuckerman

doi:10.1021/ct050337x

Resolution exchange simulation with incremental coarsening

Edward Lyman, Daniel M. Zuckerman

Biomedical Engineering

Research output: Contribution to journal › Article › peer-review

57 Scopus citations

Abstract

We previously developed an algorithm, called "resolution exchange", which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations. Here, we demonstrate a generally applicable incremental coarsening procedure and apply the algorithm to a larger peptide, met-enkephalin. In addition, we demonstrate a combination of resolution and temperature exchange, in which the coarser simulations are also at elevated temperatures. Both simulations are implemented in a "top-down" mode, to allow efficient allocation of CPU time among the different replicas.

Original language	English (US)
Pages (from-to)	656-666
Number of pages	11
Journal	Journal of Chemical Theory and Computation
Volume	2
Issue number	3
DOIs	https://doi.org/10.1021/ct050337x
State	Published - 2006

ASJC Scopus subject areas

Computer Science Applications
Physical and Theoretical Chemistry

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10.1021/ct050337x

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