Molecular dynamics simulations of phospholipid bilayer mechanoporation under different strain states—a comparison between GROMACS and LAMMPS
Molecular dynamics simulations of phospholipid bilayer mechanoporation under different strain states—a comparison between GROMACS and LAMMPS
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DOI：
10.1088/1361-651x/abfeaf
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发表时间：
2021
影响因子：
1.8
通讯作者：
A. Vo;M. Murphy;T. Stone;P. Phan;M. Baskes;R. Prabhu
中科院分区：
文献类型：
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作者：
A. Vo;M. Murphy;T. Stone;P. Phan;M. Baskes;R. Prabhu
根据所选择的分子动力学 (MD) 模拟器，细胞结构的纳米级变形机制可能会产生截然不同的结果。由于可用设置不同，这些不同MD模拟器的比较通常是一项复杂的任务，需要使用各种合理的参数选择来适当地转换所有配置。目前的研究旨在进行和比较两种常见MD软件包（GROMACS和LAMMPS）之间的生物分子MD模拟，其中磷脂双层在不同应变状态（等双轴、2:1非等双轴、4:1非等双轴、带状双轴和单轴拉伸）下变形。比较了各自 GROMACS 和 LAMMPS 模拟的应力-应变、孔成核和生长以及损伤行为的结果。一般来说，GROMACS 和 LAMMPS 产生相似的变形行为，包括损伤演化和应变状态对磷脂双层失效的影响。然而，与 LAMMPS 相比，GROMACS 在较低应变下成核了更多数量的孔隙，产生了较低的应力值和较高的损伤值。 GROMACS 和 LAMMPS 之间的多种不同设置选项（包括算法变化）已被认为是观察到的差异的可能解释。总的来说，这项研究将有助于未来MD研究中参数设置和模拟结果的交叉检查，特别是在磷脂双层和其他生物系统的机械损伤方面。在此基础上，通过未来的努力，GROMACS和LAMMPS以及其他MD程序可以同步开发，具有更好的可比性和重现性。
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.