Influence of simulation details on thermodynamic and transport properties in molecular dynamics of fully flexible molecular models

In this work, we examine the impact of details of molecular dynamics simulation and data analysis protocols on resulting thermodynamic and transport properties of interest in the study of lubricant components. Of particular importance is understanding how viscosity computed from the fluctuation-dissipation formalism is influenced by simulation details, including the differences obtained between employing an atomic vs. molecular formalism to describe the stress tensor, the impact of the size of timestep, and the type of integration scheme employed. Understanding how these simulation details affect the computed properties of interest helps us to establish simulation protocols for examining transport properties of low molecular weight isomers, where we hope to resolve differences in transport properties as a function of fine structural features of the molecules.