Nonlinear reaction coordinate analysis in the reweighted path ensemble.
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.
van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018WV Amsterdam, The Netherlands.
Wolfgang
W
Lechner
Jutta
J
Rogal
Jarek
J
Juraszek
Bernd
B
Ensing
Peter G
PG
Bolhuis
D001499:Bayes Theorem; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D017711:Nonlinear Dynamics; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D012996:Solutions / Q000737:chemistry
D011506:Proteins; D012996:Solutions