The force on an individual particle is the sum of the forces from all the other particles. This sum is easy to do on a computer. Because all the other particles are moving too, and so the force on a particle changes. We do this same process for each particle and that way predict how the whole group of particles will act. If you want to see more details go here .
Temperature is basically a measure of how fast the particles are moving.
When we start the simulation, we can choose the initial velocity for each particle. For high temperatures we use larger velocities, while for low temperatures we use smaller velocities. So at very high temperatures, we have a gas where the molecules fly around independently of each other. Molecular Dynamics Applications Simulations of small numbers of atoms or molecules are now used in many fields. For example molecular dynamics is used to look at protein folding, the design of new drugs, and the growth of thin films.