Here, m i is the atom mass, its acceleration, and the force acting upon it, due to the interactions with other atoms. However, such trajectory is usually not particularly relevant by itself.
Molecular dynamics is a statistical mechanics method .
Like Monte Carlo, it is a way to obtain a set of configurations distributed according to some statistical distribution function, or statistical ensemble. According to statistical physics, physical quantities are represented by averages over configurations distributed according to a certain statistical ensemble. A trajectory obtained by molecular dynamics provides such a set of configurations. Therefore, a measurements of a physical quantity by simulation is simply obtained as an arithmetic average of the various instantaneous values assumed by that quantity during the MD run. Statistical physics is the link between the microscopic behavior and thermodynamics.