Artifacts in dynamical simulations of coarse-grained model lipid bilayers

被引:0
|
作者
Jakobsen, AF [1 ]
Mouritsen, OG
Besold, G
机构
[1] Univ So Denmark, Dept Phys, Ctr Biomembrane Phys, MEMPHYS, Odense, Denmark
[2] Max Planck Inst Polymer Res, D-55128 Mainz, Germany
来源
JOURNAL OF CHEMICAL PHYSICS | 2005年 / 122卷 / 20期
关键词
D O I
10.1063/1.1900725
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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.
引用
收藏
页数:11
相关论文
共 50 条
  • [1] Coarse-grained simulations of lipid bilayers
    Stevens, MJ
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2004, 121 (23): : 11942 - 11948
  • [2] Ultra coarse-grained molecular dynamics simulations of lipid bilayers
    Carrillo, Jan Michael
    Katsaras, John
    Sumpter, Bobby
    Ashkar, Rana
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2018, 255
  • [3] Coarse-grained simulations of shock wave - lipid bilayers interactions
    Berkowitz, Max
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 248
  • [4] Coarse-grained model of titrating peptides interacting with lipid bilayers
    Tesei, Giulio
    Vazdar, Mario
    Lund, Mikael
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2018, 149 (24):
  • [5] Coarse-grained interactions between lipid bilayers
    Michaud-Agrawal, Naveen P.
    Crozier, Paul S.
    Stevens, Mark
    Woolf, Thomas B.
    [J]. BIOPHYSICAL JOURNAL, 2007, : 424A - 424A
  • [6] Interactions between carbon nanoparticles and lipid bilayers: insights from MD simulations with a coarse-grained model
    Monticelli, Luca
    Wong-Ekkabut, Jirasak
    Baoukina, Svetlana
    Tieleman, D. Peter
    [J]. BIOPHYSICAL JOURNAL, 2007, : 539A - 539A
  • [7] A polarizable coarse-grained water model for coarse-grained proteins simulations
    Ha-Duong, Tap
    Basdevant, Nathalie
    Borgis, Daniel
    [J]. CHEMICAL PHYSICS LETTERS, 2009, 468 (1-3) : 79 - 82
  • [8] Coarse-grained modeling of interactions of lipid bilayers with supports
    Hoopes, Matthew I.
    Deserno, Markus
    Longo, Margie L.
    Faller, Roland
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2008, 129 (17):
  • [9] Coarse-grained simulation of cation interactions with lipid bilayers
    Hills, Ronald
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2019, 257
  • [10] Coarse-grained simulations on interactions between spectrins and phase-separated lipid bilayers*
    Lin, Xuegui
    Chen, Xiaojie
    Liang, Qing
    [J]. CHINESE PHYSICS B, 2021, 30 (06)