Study On The Calculated Diffusion Coefficients Of Two Non-rectangular Simulation Box In Molecular Dynamics Simulation

In the process of molecular dynamics simulation,periodic boundary conditions are often used to eliminate the boundary effect.In order to simplify the calculation,most of the simulation is carried out by means of cuboid simulation box.Cuboid is used as the simulation box in the simulation,and the periodic boundary conditions will make the diffusion coefficient obtained in the simulation results smaller than that in the real experiment.Therefore,the simulation results cannot be directly compared with the real experiments,but need to be modified by adding correction factors.In this paper,the fluid diffusion theory is used as the starting point of the research,the modified formulas under several simulation boxes are given theoretically.With the help of molecular dynamics method,the diffusion motion of argon atom was simulated under different conditions,and the reliability and accuracy of the modified formula were tested rationally.In the simulation of molecular dynamics,cubes and cuboids are often used as the simulation boxes for periodic boundary conditions.In addition,there are two other types of simulation boxes to choose,namely the rhomboid dodecahedron and the truncated octahedron.Like cubes and cuboids,the latter two can completely fill a space without leaving any gaps.In addition,the shape of the latter two is closer to spherical of the former two,which makes the rhombic dodecahedron and the truncated octahedron more often used in the simulation of biomolecular solutions.Based on the analysis and study of the relevant data and research results,this paper proposes the corresponding modification scheme for the simulated molecular diffusion of rhombic dodecahedron and truncated octahedron,and calculates the correction coefficients of the corresponding simulation boxes respectively.On this basis,different simulation boxes were used to simulate the diffusion motion of argon atom under the conditions of three different densities,so as to verify the reliability and accuracy of the correction formula and correction coefficient according to the simulation results.