Theses and Dissertations

Title

Molecular dynamics simulations of phospholipid bilayers under deformation – a comparison between GROMACS and LAMMPS

Author

Anh TN Vo

Issuing Body

Mississippi State University

Advisor

To, Filip Suminto D.

Committee Member

Prabhu, Rajkumar

Committee Member

Stone, Tonya W.

Committee Member

Murphy, Michael A.

Date of Degree

12-1-2020

Original embargo terms

Visible to MSU only for 2 years||12/15/2022

Document Type

Graduate Thesis - Open Access

Major

Biomedical Engineering

Degree Name

Master of Science

College

James Worth Bagley College of Engineering

Department

Department of Agricultural and Biological Engineering

Abstract

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.

URI

https://hdl.handle.net/11668/20856

Sponsorship

060803-360645 Center for Advanced Vehicular Systems (CAVS)

Comments

phospholipid bilayers||deformation||mechanoporation||molecular dynamics||GROMACS||LAMMPS

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