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Download fileResolution Exchange Simulation with Incremental Coarsening
journal contribution
posted on 09.05.2006, 00:00 authored by Edward Lyman, Daniel M. ZuckermanWe 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.