Problem restarting simulations

[tlfobe]

When a folding simulation is ended before it writes the final structure, and is restarted at a later time, the old energy trajectory from the incomplete simulation is still left on the energy.txt file (I imagine also on the structures.txt file too). This results in these jumps shown in the energy trajectories.

Need to add a check to see if the energy file exists when the number of steps is zero. Otherwise, we should delete the old file.