We present a flexible nonlinear reaction coordinate analysis method for the transition path ensemble based on the likelihood maximization approach developed by Peters and Trout [J. Chem. Phys. 125, 054108 (2006)]. By parametrizing the reaction coordinate by a string of images in a collective variable space, we can optimize the likelihood that the string correctly models the committor data obtained from a path sampling simulation. The collective variable space with the maximum likelihood is considered to contain the best description of the reaction. The use of the reweighted path ensemble [J. Rogal et al., J. Chem. Phys. 133, 174109 (2010)] allows a complete reaction coordinate description from the initial to the final state. We illustrate the method on a z-shaped two-dimensional potential. While developed for use with path sampling, this analysis method can also be applied to regular molecular dynamics trajectories.
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7 November 2010
Research Article|
November 01 2010
Nonlinear reaction coordinate analysis in the reweighted path ensemble
Wolfgang Lechner;
Wolfgang Lechner
1van ’t Hoff Institute for Molecular Sciences,
University of Amsterdam
, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
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Jutta Rogal;
Jutta Rogal
2Interdisciplinary Centre for Advanced Materials Simulation (ICAMS),
Ruhr University Bochum
, 44780 Bochum, Germany
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Jarek Juraszek;
Jarek Juraszek
3
Spanish National Cancer Research Centre (CNIO)
, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
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Bernd Ensing;
Bernd Ensing
1van ’t Hoff Institute for Molecular Sciences,
University of Amsterdam
, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
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Peter G. Bolhuis
Peter G. Bolhuis
a)
1van ’t Hoff Institute for Molecular Sciences,
University of Amsterdam
, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands
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a)
Electronic mail: [email protected].
J. Chem. Phys. 133, 174110 (2010)
Article history
Received:
April 29 2010
Accepted:
September 02 2010
Connected Content
A companion article has been published:
The reweighted path ensemble
Citation
Wolfgang Lechner, Jutta Rogal, Jarek Juraszek, Bernd Ensing, Peter G. Bolhuis; Nonlinear reaction coordinate analysis in the reweighted path ensemble. J. Chem. Phys. 7 November 2010; 133 (17): 174110. https://doi.org/10.1063/1.3491818
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