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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 25, Number 4
BKCSDE 25(4)
April 20, 2004 

 
Title
Canonical Sampling Method for Initial Conditions for Reactive Flux Calculations Using Nose-Hoover Chains
Author
Song Hi Lee*, Youngshang Pak*
Keywords
Molecular dynamics simulation, Canonical sampling, Reactive flux, Nose-Hoover chain dynamics, Diels-Alder reaction
Abstract
Canonical sampling method has been presented to generate the initial conditions for reactive flux studies of organic reactions in water. Velocity Verlet version of Nose-Hoover chain dynamics algorithm has been employed to sample the initial conditions according to canonical distribution. The unstable normal mode of a transition state has been introduced to define a dividing plane separating reactant and product regions in reaction processes. This method has been implemented and tested for the case Diels-Alder reaction of methyl vinyl ketone (MVK) and cyclopentadiene (CPD) in water, providing a reliable tool for further reactive flux molecular dynamics studies in condensed media.
Page
533 - 538
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