For any numerical simulation, we need to have a initial state to begin the simulation. So we need to set the initial environment values at the beginning of simulation. The initial condition of a numerical simulation thus gives a initial state for the simulation region. The system evolution will start from this initial condition.
The initial condition should be able to reflect the real physical environment, at least it should be an acceptable simplification of the real environment.
In many cases, we can decide the initial values of the simulation region directly. But in some other cases, the initial states are so complex that it is very difficult to give the initial condition directly. So we need some other methods to derive the initial condition. For example, in global MHD simulation, generally we need to run a specific program first to determine the general configuration of magnetosphere. Only after that can we use the resulting configuration as the initial condition for the further simulation.