Annealed importance sampling of peptides.
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.
Lyman
Edward
E
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.
Zuckerman
Daniel M
DM
D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D002627:Chemistry, Physical / Q000379:methods*; D007930:Leucine / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D015233:Models, Statistical; D010455:Peptides / Q000737:chemistry*; D011489:Protein Denaturation; D017510:Protein Folding; D012984:Software; D013696:Temperature; D013816:Thermodynamics
D010455:Peptides; D007930:Leucine; D000409:Alanine