Remove complexated ions from trajectories and two minor fixes to post-processing

This MR implements the following three fixes:

1. As gmx_MMPBSA cannot handle complexated ions correctly, they are removed from the output trajectories during post-processing. However, simulation.xtc still contains the complexated ions because the entire set of input files would have to be re-created and all simulations would have to be re-run to change this. Therefore, it proved easiest to first post-process the trajectory with ions (remove pbc etc.) and then, if needed, remove the complexated ions and update all files in a final post-processing step.
2. Before we added the equilibration, we used to discard some initial frames of simulation.xtc. These lines were already commented out, but they are now removed completely for clarity.
3. In a few cases, the protein-ligand complex was still broken across periodic boundaries after post-processing. This happens if the initial structure of the simulation is already broken across the periodic boundaries. To avoid this, the first structure of simulation.xtc is now replaced with the input structure of the equilibration step when pbc are removed.