Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

Published: 7 Oct 2016 | Version 1 | DOI: 10.17632/4v53nkv5hc.1
Contributor(s):
  • S.-P. Fu,
    S.-P. Fu
    New Jersey Institute of Technology
  • Z. Peng,
    Z. Peng
    University of Notre Dame
  • H. Yuan,
    H. Yuan
    University of Rhode Island
  • R. Kfoury,
    R. Kfoury
    University of Rhode Island
  • Y.-N. Young
    Y.-N. Young
    New Jersey Institute of Technology

Description of this data

Lipid bilayer membranes have been extensively studied by coarse-grained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarse-graining, where several lipids are coarse-grained into a particle of size 4∼6 nm so that there is only one particle in the thickness direction. Yuan et al. proposed a pair-potential between these one-particle-thick coarse-grained lipid particles to capture the mechanical properties of a lipid bilayer membrane, such as gel-fluid-gas phase transitions of lipids, diffusion, and bending rigidity Yuan et al. (2010). In this work we implement such an interaction potential in LAMMPS to simulate large-scale lipid systems such as a giant unilamminar vesicle (GUV) and red blood cells (RBCs). We also consider the effect of cytoskeleton on the lipid membrane dynamics as a model for RBC dynamics, and incorporate coarse-grained water molecules to account for hydrodynamic interactions. The interaction between the coarse-grained water molecules (explicit solvent molecules) is modeled as a Lennard-Jones (L-J) potential. To demonstrate that the proposed methods do capture the observed dynamics of vesicles and RBCs, we focus on two sets of LAMMPS simulations: 1. Vesicle shape transitions with enclosed volume; 2. RBC shape transitions with different enclosed volume. Finally utilizing the parallel computing capability in LAMMPS, we provide some timing results for parallel coarse-grained simulations to illustrate that it is possible to use LAMMPS to simulate large-scale realistic complex biological membranes for more than 1 ms.

Experiment data files

peer reviewed

This data is associated with the following peer reviewed publication:

Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS

Cite this article

S.-P. Fu, Z. Peng, H. Yuan, R. Kfoury, Y.-N. Young, Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS, February 2017, Volume 210, Pages 193-203, ISSN 00104655, http://dx.doi.org/10.1016/j.cpc.2016.09.018

Published in: Computer Physics Communications

Latest version

  • Version 1

    2016-10-07

    Published: 2016-10-07

    DOI: 10.17632/4v53nkv5hc.1

    Cite this dataset

    Fu, S.-P.; Peng, Z.; Yuan, H.; Kfoury, R.; Young, Y.-N. (2016), “Lennard-Jones type pair-potential method for coarse-grained lipid bilayer membrane simulations in LAMMPS”, Mendeley Data, v1 http://dx.doi.org/10.17632/4v53nkv5hc.1

Categories

Natural Sciences

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GPLv3 Learn more

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