Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulations, but they subtly alter the phase space distribution. In a recent letter of a related title in this journal, Wong and York J. Chem. Theory Comput. 2012, 8, 3998â4003 suggest replacing Fixmanâs mass-metric correction with its inverse and adding a Jacobian contribution to the potential of mean constraint force. This letter refutes both suggestions, discusses the underlying interpretation problems, and provides supporting numerical simulations.
%0 Journal Article
%1 doi:10.1021/ct400134d
%A den Otter, Wouter K.
%D 2013
%J Journal of Chemical Theory and Computation
%K Carlo Monte chemistry constraint coordinate dynamics integral mathematics mechanics molecular physics reaction statistical unread
%N 9
%P 3861-3865
%R 10.1021/ct400134d
%T Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile
%U http://pubs.acs.org/doi/abs/10.1021/ct400134d
%V 9
%X Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulations, but they subtly alter the phase space distribution. In a recent letter of a related title in this journal, Wong and York J. Chem. Theory Comput. 2012, 8, 3998â4003 suggest replacing Fixmanâs mass-metric correction with its inverse and adding a Jacobian contribution to the potential of mean constraint force. This letter refutes both suggestions, discusses the underlying interpretation problems, and provides supporting numerical simulations.
@article{doi:10.1021/ct400134d,
abstract = { Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulations, but they subtly alter the phase space distribution. In a recent letter of a related title in this journal, Wong and York [J. Chem. Theory Comput. 2012, 8, 3998â4003] suggest replacing Fixmanâs mass-metric correction with its inverse and adding a Jacobian contribution to the potential of mean constraint force. This letter refutes both suggestions, discusses the underlying interpretation problems, and provides supporting numerical simulations. },
added-at = {2013-09-24T15:02:53.000+0200},
author = {den Otter, Wouter K.},
biburl = {https://www.bibsonomy.org/bibtex/25e666385bb4dedd4cd27b6783f48ab73/drmatusek},
doi = {10.1021/ct400134d},
eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct400134d},
interhash = {8ad6d32f90bac1b1df7d0145bafbd351},
intrahash = {5e666385bb4dedd4cd27b6783f48ab73},
journal = {Journal of Chemical Theory and Computation},
keywords = {Carlo Monte chemistry constraint coordinate dynamics integral mathematics mechanics molecular physics reaction statistical unread},
month = sep,
number = 9,
pages = {3861-3865},
timestamp = {2013-09-24T15:02:53.000+0200},
title = {Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile},
url = {http://pubs.acs.org/doi/abs/10.1021/ct400134d},
volume = 9,
year = 2013
}