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

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∼6nm 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 unilamellar 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.Program summaryProgram Title: fluidmembraneProgram Files doi:http://dx.doi.org/10.17632/4v53nkv5hc.1Licensing provisions: GNU GPLv3Programming language: C++.Nature of problem:A pair-potential function for simulating the shape transition of fluid vesicles and the resting shapes of red blood cells.Program Solution method:Nosé-Hoover thermostat and Berendsen pressure coupling algorithms.External routines/libraries: LAMMPSSubprograms used: create_rbc_with_water (MATLAB), bond_harmonic1 (C++), in_example (LAMMPS input script).