title: Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water.
abstract: Trivial trajectory parallelization of multicanonical molecular dynamics (TTP-McMD) explores the conformational space of a biological system with multiple short runs of McMD starting from various initial structures. This method simply connects (i.e., trivially parallelizes) the short trajectories and generates a long trajectory. First, we theoretically prove that the simple trajectory connection satisfies a detailed balance automatically. Thus, the resultant long trajectory is regarded as a single multicanonical trajectory. Second, we applied TTP-McMD to an alanine decapeptide with an all-atom model in explicit water to compute a free-energy landscape. The theory imposes two requirements on the multiple trajectories. We have demonstrated that TTP-McMD naturally satisfies the requirements. The TTP-McMD produces the free-energy landscape considerably faster than a single-run McMD does. We quantitatively showed that the accuracy of the computed landscape increases with increasing the number of multiple runs. Generally, the free-energy landscape of a large biological system is unknown a priori. The current method is suitable for conformational sampling of such a large system to reduce the waiting time to obtain a canonical ensemble statistically reliable.
authors.affiliation: Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
authors.forename: Jinzen
authors.initials: J
authors.lastname: Ikebe
authors.forename: Koji
authors.initials: K
authors.lastname: Umezawa
authors.forename: Narutoshi
authors.initials: N
authors.lastname: Kamiya
authors.forename: Takanori
authors.initials: T
authors.lastname: Sugihara
authors.forename: Yasushige
authors.initials: Y
authors.lastname: Yonezawa
authors.forename: Yu
authors.initials: Y
authors.lastname: Takano
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
authors.forename: Junichi
authors.initials: J
authors.lastname: Higo
mesh_terms: D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D010455:Peptides; D014867:Water