Statistical Analysis of the Effect of Simulation Time on the Results of Molecular Dynamics Studies of Food Proteins: A Study of the Ara h 6 Peanut Protein

GROMACS MD simulations of food proteins and processes are often run over relatively short simulation lengths due to their high computational power demand. As long-timescale simulations are not always feasible, the purpose of this study was to determine, statistically, how simulation time affects conclusions drawn from GROMACS MD studies of food proteins. The Ara h 6 peanut allergen, undergoing heat processing at 300 K, 350 K, 400 K and 450 K, was used as the model in this study, and 2 ns, 20 ns and 200 ns GROMACS MD simulation lengths were investigated. The statistical analysis performed, using both one-way and two-way ANOVA tests, suggested that, depending on the selected simulation length, different final conclusions may be drawn regarding the effect that thermal processing temperature has on the geometric features of the Ara h 6 allergen. This was observed for many of the geometric features used to characterize the Ara h 6 allergen in this study, including RMSD, Rg, total number of intra-peptide hydrogen bonds and SASA. An inadequate sample size was, however, identified as a major limitation in this study.