Dividing the Periodic Box into Subdivisions with Their Surroundings to Accelerate Molecular Dynamics Simulation with...

A major field of current research in chemistry and biology is the development of the tools that enable in situ analysis of complex systems. However, the long-time dynamics simulation for an extremely large system in solution is almost impossible by an all-atom force field combined with an explicit solvent model. The results show that the larger the periodic box is, the closer the properties of the system are to the experimental values. Therefore, how can we carry out simulations for systems that are fast, accurate, and large enough? A method of dividing the periodic box into subdivisions with their surroundings (DBSS) is presented here, and it clearly increases the computation speed without losing accuracy and enables the simulation of extremely large systems by strongly decreasing the dimension of the charge matrix. The DBSS method divides a single periodic box or unit in an extremely large system into several subdivisions with a suitable choice according to atomic coordinates. This method ensures that these subdivisions are always changing and allows the atoms to communicate with each other. Intermolecular communication is important for molecular properties and functions but is not possible with other fragment methods. The partial charges are calculated in each subdivision with an overlapping surrounding used to take hydrogen bond interaction between the subdivisions into account. This is an iterative process because the charge population will be recalculated at intervals during the dynamics simulations. Taking a water system as an example, each subdivision is extended by 4 Å as the surrounding. The computation time scales almost linearly with the size of the system, and the slope is small. MD simulations for several properties have been performed by the ABEEM-DBSS method. The results indicate that the ABEEM-DBSS method can accurately simulate the properties of water system, and the accuracy can reach or approach that of the experimental data or of other water potentials. Interestingly, the properties become closer to the experimental data as the sizes of the periodic box increase, further validating the need for the simulation of a large system and demonstrating the value of the DBSS method.