Basic Cell Size Dependence of Displacement for a Solvation Motor in a Lennard-Jones Solvent

Abstract

Solvation change induced by a chemical reaction can move a macromolecule in a specific direction. The hydrodynamic effect on a solvation motor was studied by using molecular dynamics simulations with a simple model. We examined the dependence of motor displacement induced by the chemical reaction on the size of the basic cell. The size dependence given by the simulation sat on a straight line as a function of the system size, and the displacement in an infinite system was estimated from the plot.

Usefulness of Higher Order of System-Size Correction for Diffusion Coefficients of Macromolecules: A Molecular Dynamics Study

“…Previous studies have reported that Eq. ( 2) is reasonable in various systems and basic cell sizes [16,17,18,19,20,21,22,23]. In principle, however, given the small size of the system, the correction value D YH1 0 must depend on 1/L due to the additional correction term (Eq.…”

“…( 2) gives us adequate D 0 for a Lennard-Jones liquid even when the system has only 27 particles [16]. This equation has been used in various systems to estimate the diffusion coefficients D 0 [18,19,20,21,22,23]. On the other hand, an additional correction term was shown as follows:…”