Abstract
Annealed importance sampling assigns equilibrium weights to a nonequilibrium sample that was generated by a simulated annealing protocol [R. M. Neal, Stat. Comput. 11, 125 (2001)]. The weights may then be used to calculate equilibrium averages, and also serve as an "adiabatic signature" of the chosen cooling schedule. In this paper we demonstrate the method on the 50-atom dileucine peptide and an alanine 5-mer, showing that equilibrium distributions are attained for manageable cooling schedules. For dileucine, as naively implemented here, the method is modestly more efficient than constant temperature simulation. The alanine application demonstrates the success of the method when there is little overlap between the high (unfolded) and low (folded) temperature distributions. The method is worth considering whenever any simulated heating or cooling is performed (as is often done at the beginning of a simulation project or during a NMR structure calculation), as it is simple to implement and requires minimal additional computational expense. Furthermore, the naive implementation presented here can be improved.
| Original language | English (US) |
|---|---|
| Article number | 065101 |
| Journal | Journal of Chemical Physics |
| Volume | 127 |
| Issue number | 6 |
| DOIs | |
| State | Published - Aug 20 2007 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry
Cite this
Annealed importance sampling of peptides. / Lyman, Edward; Zuckerman, Daniel.
In: Journal of Chemical Physics, Vol. 127, No. 6, 065101, 20.08.2007.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Annealed importance sampling of peptides
AU - Lyman, Edward
AU - Zuckerman, Daniel
PY - 2007/8/20
Y1 - 2007/8/20
N2 - Annealed importance sampling assigns equilibrium weights to a nonequilibrium sample that was generated by a simulated annealing protocol [R. M. Neal, Stat. Comput. 11, 125 (2001)]. The weights may then be used to calculate equilibrium averages, and also serve as an "adiabatic signature" of the chosen cooling schedule. In this paper we demonstrate the method on the 50-atom dileucine peptide and an alanine 5-mer, showing that equilibrium distributions are attained for manageable cooling schedules. For dileucine, as naively implemented here, the method is modestly more efficient than constant temperature simulation. The alanine application demonstrates the success of the method when there is little overlap between the high (unfolded) and low (folded) temperature distributions. The method is worth considering whenever any simulated heating or cooling is performed (as is often done at the beginning of a simulation project or during a NMR structure calculation), as it is simple to implement and requires minimal additional computational expense. Furthermore, the naive implementation presented here can be improved.
AB - Annealed importance sampling assigns equilibrium weights to a nonequilibrium sample that was generated by a simulated annealing protocol [R. M. Neal, Stat. Comput. 11, 125 (2001)]. The weights may then be used to calculate equilibrium averages, and also serve as an "adiabatic signature" of the chosen cooling schedule. In this paper we demonstrate the method on the 50-atom dileucine peptide and an alanine 5-mer, showing that equilibrium distributions are attained for manageable cooling schedules. For dileucine, as naively implemented here, the method is modestly more efficient than constant temperature simulation. The alanine application demonstrates the success of the method when there is little overlap between the high (unfolded) and low (folded) temperature distributions. The method is worth considering whenever any simulated heating or cooling is performed (as is often done at the beginning of a simulation project or during a NMR structure calculation), as it is simple to implement and requires minimal additional computational expense. Furthermore, the naive implementation presented here can be improved.
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U2 - 10.1063/1.2754267
DO - 10.1063/1.2754267
M3 - Article
VL - 127
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 6
M1 - 065101
ER -