All that said, in an NPT simulation, it usually isn't disastrous to use the last coordinate set of the trajectory and re-initialize the velocities, provided that this doesn't happen too frequently. However, your simulation seems to be only 40ps; reinitializing the velocities every 40ps would definitely classify as "too frequently" in my opinion.

And as Lennart mentioned in his first answer, I would be hard pressed to explain in detail how to extract the last coordinate set from a trajectory and start a new simulation in less time than it takes the computer to run 40ps worth of simulation, unless the simulations is incredibly slow.