Molecular dynamics (MD) are based on a algorithm, the figure below shows the basic molecular dynamics steps:

For each MD step (lines 3, 4 and 5), is necessary to integrate the Newton’s motions equation, the Verlet algorithm is widely use for this task. However, there is a important issue to tackle, the Delta T has to be small (on 1 fs order) to minimize the error and result on a correct simulation. To solve this issue is possible to use accelerated molecular dynamics.