TY - JOUR
T1 - Resolution exchange simulation with incremental coarsening
AU - Lyman, Edward
AU - Zuckerman, Daniel M.
N1 - Copyright:
Copyright 2007 Elsevier B.V., All rights reserved.
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
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U2 - 10.1021/ct050337x
DO - 10.1021/ct050337x
M3 - Article
AN - SCOPUS:33846204007
VL - 2
SP - 656
EP - 666
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
SN - 1549-9618
IS - 3
ER -