title: Communication: Simulated tempering with fast on-the-fly weight determination.
abstract: We propose an efficient method to enhance sampling in computer simulations by combining the simulated tempering algorithm with a fast on-the-fly weight determination scheme. The weights are self-updated via a trapezoid rule during the simulated tempering simulation. With our proposed scheme, simulated tempering requires neither prior trial simulations nor complicated update schemes. The advantage of our method over replica exchange molecular dynamics has been demonstrated with the study of the folding of the 20-residue alanine peptide and the aggregation of a trimer formed by the Alzheimer's peptide fragment Aβ(16-22).
authors: Laboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France. phuong.nguyen@ibpc.fr
authors: Phuong H
authors: PH
authors: Nguyen
authors: Yuko
authors: Y
authors: Okamoto
authors: Philippe
authors: P
authors: Derreumaux
mesh_terms: D000465:Algorithms; D016229:Amyloid beta-Peptides / Q000737:chemistry; D003198:Computer Simulation; D010446:Peptide Fragments / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D010455:Peptides; C417223:amyloid beta-protein (16-22)