title: Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules.
abstract: A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems.
authors.affiliation: Molecular Modeling and Simulation Group, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.
authors.forename: Jinzen
authors.initials: J
authors.lastname: Ikebe
authors.forename: Shun
authors.initials: S
authors.lastname: Sakuraba
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Kono
mesh_terms: D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011107:Polylysine / Q000737:chemistry*
chemical_list: D009842:Oligopeptides; D011107:Polylysine
keywords: all-atom model; explicit water; free energy landscape; generalized ensemble method; partial system