I am studying a grain boundary in the ZrO2-Y2O3 system. In order to make atoms move, I am applying a force to some of them. As a result of that, the whole system is moving, as the grain boundary does in particular. I have viewed this by VMD from the trajectory file.
However, I wonder if the ave/spatial fix takes into account the movement of the center of mass of the system. In other words, when I perform the fix ave/spatial and divide the simulation box into several bins, are these related to the initial box or they change with time?
Any help is welcome…