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Molecular dynamics coupled with a virtual system for effective conformational sampling
Author(s) -
Hayami Tomonori,
Kasahara Kota,
Nakamura Haruki,
Higo Junichi
Publication year - 2018
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25196
Subject(s) - molecular dynamics , reaction coordinate , umbrella sampling , computer science , sampling (signal processing) , statistical physics , canonical ensemble , dissociation (chemistry) , system dynamics , potential of mean force , biological system , chemistry , computational chemistry , physics , mathematics , artificial intelligence , monte carlo method , computer vision , statistics , filter (signal processing) , biology
An enhanced conformational sampling method is proposed: virtual‐system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free‐energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.