VMD has the capability to work with a molecular dynamics program running on another computer in order to display the results of a simulation as they are calculated. As new atomic coordinate timesteps are generated by the simulation process, they can be transferred directly over the network to VMD , which can then animate the molecule. A major new feature in VMD is the ability to add perturbative steering forces to a running simulation, which are incorporated directly into the dynamics calculation.

VMD is often used in conjunction with NAMD, which is a parallel, object oriented molecular dynamics program.