Response to "comment on 'Free energy simulations of single and double ion occupancy in gramicidin A'" [The Journal of Chemical Physics (2008) 128 (227101))

Turgut Baştuǧ; Serdar Kuyucak

doi:10.1063/1.2931571

Response to "comment on 'Free energy simulations of single and double ion occupancy in gramicidin A'" [The Journal of Chemical Physics (2008) 128 (227101))

Turgut Baştuǧ
, Serdar Kuyucak

Research output: Contribution to journal › Review article › peer-review

2 Citations (Scopus)

Abstract

We respond to the criticism that one-dimensional (1D) construction of the potential of mean force (PMF) of ions in channels is flowed. Comparison of the 1D PMF results in the gramicidin A channel with independent free energy difference calculations obtained by using the free energy perturbation and thermodynamic integration methods shows complete agreement, thus providing a justifications for the 1D PMF approximation.

Original language	English
Article number	227102
Journal	Journal of Chemical Physics
Volume	128
Issue number	22
DOIs	https://doi.org/10.1063/1.2931571
Publication status	Published - 2008
Externally published	Yes

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10.1063/1.2931571

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@article{336aff65714147bda6ab501fbf9e2ab3,

title = "Response to {"}comment on 'Free energy simulations of single and double ion occupancy in gramicidin A'{"} [The Journal of Chemical Physics (2008) 128 (227101))",

abstract = "We respond to the criticism that one-dimensional (1D) construction of the potential of mean force (PMF) of ions in channels is flowed. Comparison of the 1D PMF results in the gramicidin A channel with independent free energy difference calculations obtained by using the free energy perturbation and thermodynamic integration methods shows complete agreement, thus providing a justifications for the 1D PMF approximation.",

author = "Turgut Ba{\c s}tuǧ and Serdar Kuyucak",

year = "2008",

doi = "10.1063/1.2931571",

language = "English",

volume = "128",

journal = "Journal of Chemical Physics",

issn = "0021-9606",

publisher = "American Institute of Physics",

number = "22",

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TY - JOUR

T1 - Response to "comment on 'Free energy simulations of single and double ion occupancy in gramicidin A'" [The Journal of Chemical Physics (2008) 128 (227101))

AU - Baştuǧ, Turgut

AU - Kuyucak, Serdar

PY - 2008

Y1 - 2008

N2 - We respond to the criticism that one-dimensional (1D) construction of the potential of mean force (PMF) of ions in channels is flowed. Comparison of the 1D PMF results in the gramicidin A channel with independent free energy difference calculations obtained by using the free energy perturbation and thermodynamic integration methods shows complete agreement, thus providing a justifications for the 1D PMF approximation.

AB - We respond to the criticism that one-dimensional (1D) construction of the potential of mean force (PMF) of ions in channels is flowed. Comparison of the 1D PMF results in the gramicidin A channel with independent free energy difference calculations obtained by using the free energy perturbation and thermodynamic integration methods shows complete agreement, thus providing a justifications for the 1D PMF approximation.

UR - https://www.scopus.com/pages/publications/45149113841

U2 - 10.1063/1.2931571

DO - 10.1063/1.2931571

M3 - Review article

AN - SCOPUS:45149113841

SN - 0021-9606

VL - 128

JO - Journal of Chemical Physics

JF - Journal of Chemical Physics

IS - 22

M1 - 227102

ER -

Response to "comment on 'Free energy simulations of single and double ion occupancy in gramicidin A'" [The Journal of Chemical Physics (2008) 128 (227101))

Abstract

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