Printing too many frames in trajectory files

[GregorySchwing]

Describe the bug
A frame is duplicated in a trajectory file. We are unable to print out a single frame at the end of a simulation. We desire to run a n step simulation, and print to trajectory every n steps. This should only produce 1 frame, but it is producing > 1.

To Reproduce
Run a simulation for 10 steps. Set DCDFreq to 10 and CoordinatesFreq to 10.

Expected behavior
1 frame should be printed, the coordinates at the end of the simulation.

[bc118]

This may want to be fixed in the future. For example, when we restart a simulation, the last frame of old previous simulation and the first frame of the restarted simulation will be the same. If your counting steps it will shift them to be off, by having duplicate trajectories.

Ideally, we want the initial trajectory to be recorded for the start of the simulation, but not on a restart. If we are just stabilizing a system, it is likely best just to start from an equilibrium pdb and psf, and not do a restart for MC. Alternatively, we may want an option here.