My officemate ran into some problems with a topology file that we've generated because of specific situations where the pdb/psf pair is loaded in the wrong order, or the psf was generated in such a way that VMD is not detecting fragments consistently with how GROMACS views a molecule. These commits add this error checking for these potential input problems, as well as add the paper reference to the generated topology files.
My officemate ran into some problems with a topology file that we've generated because of specific situations where the pdb/psf pair is loaded in the wrong order, or the psf was generated in such a way that VMD is not detecting fragments consistently with how GROMACS views a molecule. These commits add this error checking for these potential input problems, as well as add the paper reference to the generated topology files.