problem with GROMACS two-step topologies

[skfegan]

As reported by Laura Perez. When a morph involves both insertion and deletion of atoms, for GROMACS this needs to be done in two steps. FESetup is creating morph1 and morph2 files, but creating charges on some dummy atoms so that the removal and insertion of atoms is being mixed rather than as two separate steps. This is leading to unstable simulations.