Figure out what to do with three clashing molecules

[tomnewport]

If A clashes with B, B with C and C with A then alchembed won't work. Here are some ideas:

• Do a simple (A alchembed B) alchembed C?
  • Could be difficult, particles will wander in vacuum
  • Dummy particles to prevent diffusion?
• Combine B and C and hope for the best?
• Do A alchembed B then alchembed C and just don't worry about diffusion
• Reduce cutoff distance so clash threshold is higher