Annealed importance sampling of dileucine peptide

Details Annealed importance sampling of dileucine peptide Annealed importance sampling of dileucine peptide

2007-04-03

arxiv.org/abs/0704.0464v1

Biology

Quantitative Biology

Biomolecules

Scientific paper

10.1063/1.2754267

Annealed importance sampling is a means to assign equilibrium weights to a nonequilibrium sample that was generated by a simulated annealing protocol. 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, showing that equilibrium distributions are attained for manageable cooling schedules. For this system, as naively implemented here, the method is modestly more efficient than constant temperature simulation. However, 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 an NMR structure calculation), as it is simple to implement and requires minimal additional CPU expense. Furthermore, the naive implementation presented here can be improved.

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