Molecular dynamics simulations of phospholipid bilayer mechanoporation under different strain states-a comparison between GROMACS and LAMMPS

ATN Vo and MA Murphy and TW Stone and PK Phan and MI Baskes and RK Prabhu, MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, 29, 055015 (2021).

DOI: 10.1088/1361-651X/abfeaf

Nanoscale deformation mechanisms of cellular structures could render drastically different results depending on the molecular dynamics (MD) simulator chosen. Due to different available settings, the comparison of these different MD simulators is typically an intricate task, requiring that all configurations be converted appropriately with a variety of reasonable parameter choices. The current study aims to perform and compare MD simulations of biomolecules between two common MD software packages (GROMACS and LAMMPS), in which a phospholipid bilayer is deformed under different strain states (equibiaxial, 2:1 non- equibiaxial, 4:1 non-equibiaxial, strip biaxial and uniaxial tension). The results for the stress-strain, pore nucleation and growth, and damage behavior are compared between the respective GROMACS and LAMMPS simulations. In general, GROMACS and LAMMPS produced similar deformation behavior, including damage evolution and the effect of strain state on phospholipid bilayer failure. However, GROMACS nucleated a greater number of pores at lower strains, produced lower stress values and higher damage values than LAMMPS. Multiple different setting options between GROMACS and LAMMPS, including algorithm variations, have been considered as possible explanations for the observed differences. Overall, this study will aid in the cross-check of parameter settings and simulation results in future MD research, particularly on the mechanical damage of phospholipid bilayers and other biological systems. Based on that, with future efforts, GROMACS and LAMMPS, as well as other MD programs, could be exploited synchronously with better comparability and reproducibility.

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