Model of nanoscale deformation mechanisms of cellular structures could render different results depending on the molecular dynamics (MD) simulator chosen. Also, the comparison of different MD simulators is typically an intricate task, requiring all configurations be converted appropriately with available parameter choices. This study aims to perform and compare MD simulations between two MD programs (GROMACS and LAMMPS), in which a phospholipid bilayer is deformed under different strain states. The two systems produced similar deformation behaviors and strain state effect on bilayer failure. However, GROMACS produced more pores at lower strains, lower stress, and higher damage values. Multiple setting options and algorithm variations have been considered as possible explanations for the differences. Overall, the study aids in the cross-check of parameter settings and simulation results in MD research, particularly on the mechanical damage of bilayer membranes. Besides, based on that, GROMACS and LAMMPS could be further exploited with better reproducibility.
| Identifer | oai:union.ndltd.org:MSSTATE/oai:scholarsjunction.msstate.edu:td-4186 |
| Date | 25 November 2020 |
| Creators | Vo, Anh TN |
| Publisher | Scholars Junction |
| Source Sets | Mississippi State University |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | Theses and Dissertations |
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