Effect of the Simulation Box Size and Precipitant Concentration on the Behavior of Tetragonal Lysozyme Dimer

Abstract

Abstract The 10-nanosecond simulation of a lysozyme dimer, which is a fragment of the tetragonal lysozyme crystal structure, has been carried out by the molecular dynamics method at different simulation box sizes and precipitant concentrations in a solution. The dimer stability has been estimated by calculating the root-mean-square fluctuations of protein atoms. It is shown that the box size does not significantly affect the mobility of protein atoms on a relatively short trajectory, while the effect of the precipitant concentration on this trajectory is noticeable.