Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide

The Journal of Chemical Physics
Wenjin Li

Abstract

Transition path ensemble consists of reactive trajectories and possesses all the information necessary for the understanding of the mechanism and dynamics of important condensed phase processes. However, quantitative description of the properties of the transition path ensemble is far from being established. Here, with numerical calculations on a model system, the equipartition terms defined in thermal equilibrium were for the first time estimated in the transition path ensemble. It was not surprising to observe that the energy was not equally distributed among all the coordinates. However, the energies distributed on a pair of conjugated coordinates remained equal. Higher energies were observed to be distributed on several coordinates, which are highly coupled to the reaction coordinate, while the rest were almost equally distributed. In addition, the ensemble-averaged energy on each coordinate as a function of time was also quantified. These quantitative analyses on energy distributions provided new insights into the transition path ensemble.

References

May 10, 2000·Proceedings of the National Academy of Sciences of the United States of America·P G BolhuisD Chandler
Apr 25, 2002·Annual Review of Physical Chemistry·Peter G BolhuisPhillip L Geissler
Oct 3, 2003·Proceedings of the National Academy of Sciences of the United States of America·Peter G Bolhuis
Jul 23, 2004·The Journal of Chemical Physics·Gerhard Hummer
Apr 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Robert B Best, Gerhard Hummer
Oct 6, 2005·Journal of the American Chemical Society·Jodi E Basner, Steven D Schwartz
Apr 22, 2006·The Journal of Chemical Physics·Ao MaAaron R Dinner
Jul 21, 2006·The Journal of Physical Chemistry. B·Weinan EEric Vanden-Eijnden
Jul 21, 2006·The Journal of Physical Chemistry. B·Ao Ma, Aaron R Dinner
Sep 1, 2006·The Journal of Chemical Physics·Baron Peters, Bernhardt L Trout
Sep 13, 2006·The Journal of Chemical Physics·Philipp MetznerEric Vanden-Eijnden
Oct 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·J Juraszek, P G Bolhuis
Jul 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Sara L Quaytman, Steven D Schwartz
Jul 28, 2007·The Journal of Chemical Physics·Baron PetersBernhardt L Trout
Nov 6, 2007·The Journal of Chemical Physics·Ernesto E Borrero, Fernando A Escobedo
Nov 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Bin W ZhangDaniel M Zuckerman
Mar 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jie HuAaron R Dinner
Apr 25, 2009·The Journal of Chemical Physics·Dimitri Antoniou, Steven D Schwartz
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jocelyne VreedePeter G Bolhuis
Nov 11, 2010·Journal of the American Chemical Society·Wenjin Li, Frauke Gräter
Feb 22, 2011·The Journal of Physical Chemistry. B·Dimitri Antoniou, Steven D Schwartz
Apr 5, 2011·The Journal of Chemical Physics·Mary A RohrdanzCecilia Clementi
Nov 18, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Rosalind J AllenPieter Rein Ten Wolde
Aug 25, 2011·The Journal of Physical Chemistry. B·Sergei V Krivov
Feb 15, 2013·The Journal of Chemical Physics·Baron PetersJoan-Emma Shea
Sep 10, 2014·Molecular Simulation·Wenjin Li, Ao Ma
Mar 10, 2016·Proceedings of the National Academy of Sciences of the United States of America·Robert B Best, Gerhard Hummer
Mar 24, 2016·The Journal of Chemical Physics·Wenjin Li, Ao Ma
Apr 10, 2016·The Journal of Chemical Physics·Wenjin Li, Ao Ma

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