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Resolution Exchange Simulation with Incremental Coarsening

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journal contribution
posted on 09.05.2006, 00:00 by Edward Lyman, Daniel M. Zuckerman
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.