Molecular dynamics coupled with a virtual system for effective conformational sampling

Journal of Computational Chemistry
Tomonori HayamiJunichi Higo

Abstract

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.

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Citations

Nov 18, 2018·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Dmitry I SharapaYury Minenkov
Oct 15, 2019·Protein Engineering, Design & Selection : PEDS·Junichi HigoHaruki Nakamura
Nov 27, 2020·Biophysics and Physicobiology·Kota KasaharaJunichi Higo

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