Method to use alchembed on two separate .gro files

[tomnewport]

This will need as inputs:

• An alchex config object
• A simulation container
• Topology for system1
• Topology for system2
• Structure for system1
• Structure for system2
• Additional parameters
• A working directory

(note that system1 must include parameters for system2)

Next we need to:

1. For both systems:
   1. Obtain preprocessed topologies using grompp
   2. Build moltypes using topcat
2. Update resids in combined topologies
3. Modify system1 topology to include system1, system2 as moltypes
4. Write the alchembed.mdp file with any modifications, and couple-moltype set to system2
5. GROMPP files
6. MDRUN files
7. Build combined topology and structure
   • Re-order residues
   • Renumber atoms
   • Write order to topology file