Minimum Acceptable Simulation Box Size Based on a Comparison of the Stability of Lysozyme Oligomers Using Molecular Dynamics

Abstract

The duration of a simulation directly depends on the size of the system under study: the larger its volume, the longer the calculations. Using a simulation box of minimal size is the most efficient in terms of calculation speed; however, its reduction is permissible only as long as it does not lead to a loss of accuracy of the results. To establish the threshold to which a box can be reduced, the molecular dynamics of lysozyme dimers and hexamers in a crystallization solution is modelled in simulation boxes of different sizes. Since dimers (and octamers) are present in lysozyme crystallization solutions, but hexamers (and tetramers) are absent, a comparison of their stability makes it possible to determine the correctness of the simulation results in each box. It is found that the dimer is more stable than the hexamer in all boxes under consideration, the smallest of which is set so that the minimum distance between the protein atoms and the box face is 1 nm. Thus, this offset is the minimum permissible one in the study of protein crystallization solutions.