Artifacts in dynamical simulations of coarse-grained model lipid bilayers

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

Standard

Artifacts in dynamical simulations of coarse-grained model lipid bilayers. / Jakobsen, Ask F.; Mouritsen, Ole G.; Besold, Gerhard.

In: Journal of Chemical Physics, Vol. 122, No. 20, 204901, 22.05.2005.

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

Harvard

Jakobsen, AF, Mouritsen, OG & Besold, G 2005, 'Artifacts in dynamical simulations of coarse-grained model lipid bilayers', Journal of Chemical Physics, vol. 122, no. 20, 204901. https://doi.org/10.1063/1.1900725

APA

Jakobsen, A. F., Mouritsen, O. G., & Besold, G. (2005). Artifacts in dynamical simulations of coarse-grained model lipid bilayers. Journal of Chemical Physics, 122(20), [204901]. https://doi.org/10.1063/1.1900725

Vancouver

Jakobsen AF, Mouritsen OG, Besold G. Artifacts in dynamical simulations of coarse-grained model lipid bilayers. Journal of Chemical Physics. 2005 May 22;122(20). 204901. https://doi.org/10.1063/1.1900725

Author

Jakobsen, Ask F. ; Mouritsen, Ole G. ; Besold, Gerhard. / Artifacts in dynamical simulations of coarse-grained model lipid bilayers. In: Journal of Chemical Physics. 2005 ; Vol. 122, No. 20.

Bibtex

@article{d46245cac83d4166bd166f0423ccc7bd,
title = "Artifacts in dynamical simulations of coarse-grained model lipid bilayers",
abstract = "With special focus on dissipative particle dynamics simulations of anisotropic and complex soft matter, such as lipid bilayers in water, we have investigated the occurrence of artifacts in the results obtained from dynamical simulations of coarse-grained particle-based models. The particles are modeled by beads that interact via soft repulsive conservative forces (as defined in dissipative particle dynamics simulations), harmonic bond potentials, as well as bending potentials imparting stiffness to the lipid tails. Two different update schemes are investigated: dissipative particle dynamics with a velocity-Verlet-like integration scheme [G. Besold, I. Vattulainen, M. Karttunen, and J. M. Polson, Phys. Rev. E 63, R7611 (2000)] and Lowe-Andersen thermostatting [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] with the standard velocity-Verlet integration algorithm. By varying the integration time step, we examine various physical quantities, in particular pressure profiles and kinetic bead temperatures, for their sensitivity to artifacts caused by the specific combination of integration technique and the thermostat. We then propose a simple fingerprint method that allows monitoring the presence of simulation artifacts.",
author = "Jakobsen, {Ask F.} and Mouritsen, {Ole G.} and Gerhard Besold",
year = "2005",
month = may,
day = "22",
doi = "10.1063/1.1900725",
language = "English",
volume = "122",
journal = "The Journal of Chemical Physics",
issn = "0021-9606",
publisher = "American Institute of Physics",
number = "20",

}

RIS

TY - JOUR

T1 - Artifacts in dynamical simulations of coarse-grained model lipid bilayers

AU - Jakobsen, Ask F.

AU - Mouritsen, Ole G.

AU - Besold, Gerhard

PY - 2005/5/22

Y1 - 2005/5/22

N2 - With special focus on dissipative particle dynamics simulations of anisotropic and complex soft matter, such as lipid bilayers in water, we have investigated the occurrence of artifacts in the results obtained from dynamical simulations of coarse-grained particle-based models. The particles are modeled by beads that interact via soft repulsive conservative forces (as defined in dissipative particle dynamics simulations), harmonic bond potentials, as well as bending potentials imparting stiffness to the lipid tails. Two different update schemes are investigated: dissipative particle dynamics with a velocity-Verlet-like integration scheme [G. Besold, I. Vattulainen, M. Karttunen, and J. M. Polson, Phys. Rev. E 63, R7611 (2000)] and Lowe-Andersen thermostatting [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] with the standard velocity-Verlet integration algorithm. By varying the integration time step, we examine various physical quantities, in particular pressure profiles and kinetic bead temperatures, for their sensitivity to artifacts caused by the specific combination of integration technique and the thermostat. We then propose a simple fingerprint method that allows monitoring the presence of simulation artifacts.

AB - With special focus on dissipative particle dynamics simulations of anisotropic and complex soft matter, such as lipid bilayers in water, we have investigated the occurrence of artifacts in the results obtained from dynamical simulations of coarse-grained particle-based models. The particles are modeled by beads that interact via soft repulsive conservative forces (as defined in dissipative particle dynamics simulations), harmonic bond potentials, as well as bending potentials imparting stiffness to the lipid tails. Two different update schemes are investigated: dissipative particle dynamics with a velocity-Verlet-like integration scheme [G. Besold, I. Vattulainen, M. Karttunen, and J. M. Polson, Phys. Rev. E 63, R7611 (2000)] and Lowe-Andersen thermostatting [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] with the standard velocity-Verlet integration algorithm. By varying the integration time step, we examine various physical quantities, in particular pressure profiles and kinetic bead temperatures, for their sensitivity to artifacts caused by the specific combination of integration technique and the thermostat. We then propose a simple fingerprint method that allows monitoring the presence of simulation artifacts.

UR - http://www.scopus.com/inward/record.url?scp=34548057237&partnerID=8YFLogxK

U2 - 10.1063/1.1900725

DO - 10.1063/1.1900725

M3 - Journal article

C2 - 15945771

AN - SCOPUS:34548057237

VL - 122

JO - The Journal of Chemical Physics

JF - The Journal of Chemical Physics

SN - 0021-9606

IS - 20

M1 - 204901

ER -

ID: 230978468