Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile

Wouter K. den Otter

doi:10.1021/ct400134d

Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile

Wouter K. den Otter

Research output: Contribution to journal › Article › Academic › peer-review

20 Citations (Scopus)

1 Downloads (Pure)

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, 3998–4003] suggest replacing Fixman’s 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.

Original language	Undefined
Pages (from-to)	3861-3865
Number of pages	5
Journal	Journal of chemical theory and computation
Volume	9
Issue number	9
DOIs	https://doi.org/10.1021/ct400134d
Publication status	Published - 2013

Keywords

IR-90013
METIS-298376

Access to Document

10.1021/ct400134d

Cite this

@article{af9002ddc940430ca0bc34e19d727b98,

title = "Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile",

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, 3998–4003] suggest replacing Fixman{\textquoteright}s 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.",

keywords = "IR-90013, METIS-298376",

author = "{den Otter}, {Wouter K.}",

year = "2013",

doi = "10.1021/ct400134d",

language = "Undefined",

volume = "9",

pages = "3861--3865",

journal = "Journal of chemical theory and computation",

issn = "1549-9618",

publisher = "American Chemical Society",

number = "9",

}

TY - JOUR

T1 - Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile

AU - den Otter, Wouter K.

PY - 2013

Y1 - 2013

N2 - 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, 3998–4003] suggest replacing Fixman’s 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.

AB - 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, 3998–4003] suggest replacing Fixman’s 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.

KW - IR-90013

KW - METIS-298376

U2 - 10.1021/ct400134d

DO - 10.1021/ct400134d

M3 - Article

SN - 1549-9618

VL - 9

SP - 3861

EP - 3865

JO - Journal of chemical theory and computation

JF - Journal of chemical theory and computation

IS - 9

ER -