Molecular dynamics simulations of phospholipid bilayers under deformation – a comparison between GROMACS and LAMMPS
Mississippi State University
To, Filip Suminto D.
Stone, Tonya W.
Murphy, Michael A.
Date of Degree
Original embargo terms
Visible to MSU only for 2 years||12/15/2022
Graduate Thesis - Open Access
Master of Science
James Worth Bagley College of Engineering
Department of Agricultural and Biological Engineering
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.
060803-360645 Center for Advanced Vehicular Systems (CAVS)
Vo, Anh TN, "Molecular dynamics simulations of phospholipid bilayers under deformation – a comparison between GROMACS and LAMMPS" (2020). Theses and Dissertations. 3187.