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 | |
| State | Published - Dec 1 2006 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Computer Science Applications
- Physical and Theoretical Chemistry
Cite this
Resolution exchange simulation with incremental coarsening. / Lyman, Edward; Zuckerman, Daniel.
In: Journal of Chemical Theory and Computation, Vol. 2, No. 3, 01.12.2006, p. 656-666.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Resolution exchange simulation with incremental coarsening
AU - Lyman, Edward
AU - Zuckerman, Daniel
PY - 2006/12/1
Y1 - 2006/12/1
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.
UR - http://www.scopus.com/inward/record.url?scp=33846204007&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33846204007&partnerID=8YFLogxK
U2 - 10.1021/ct050337x
DO - 10.1021/ct050337x
M3 - Article
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 -