Bigger Isn't Always Better: Comparing System Size, Hydration, and Software for Lipid Membrane Analysis

Abstract

The structural and dynamic properties of membranes are known to vary with bilayer size and hydration. While Molecular Dynamic (MD) simulations are a powerful tool for studying cellular membrane systems, the results can be sensitive to the analysis work-flow and software. In this study, all-atom MD simulations (500 ns) were conducted on systems of 256, 512, and 1024 POPC lipids at 40, 80, and 160 waters per lipid. With these simulations, a two-fold study was performed: (1) to assess the convergence of structural and dynamic properties of POPC bilayers as a function of membrane size and hydration level using CPPTRAJ (CPP), including area per lipid (APL), bilayer thickness, order parameter, headgroup orientation, and lateral diffusion, and (2) to compare the analysis output and performance of four software packages: CPP, GROMACS (GRO), MDAnalysis (MDA), and LiPyphilic (LiP). For the first objective, our results show that the average values of the bilayer thickness, order parameter, and headgroup orientation are largely independent of the size and hydration levels studied. In contrast, lateral diffusion coefficient was sensitive to both size and hydration. We found that increasing the system size primarily decreased the statistical variance of the APL and thickness. For the second objective, all four packages produced consistent results for APL and thickness, with the most significant discrepancy being a known artifact from the gmx order tool when applied to unsaturated carbons. Performance bench-marks identified CPP as the fastest serial tool for all properties, whereas parallelization benefited MDA and LiP in some metrics. These findings provide a practical roadmap, demonstrating that moderately sized systems (e.g., 256L), combined with an optimized tool such as CPP, offer an efficient workflow for membrane structural property analysis.