Design Philosophy

At this point this is just a jumble of decisions

1. Multi-layer approach: high level API for casual users, gmx commands are also exposed for power users
2. Auto-generating the overall topology. Topology file generation must be cheap.
3. Molecule topologies are to be given by the user (i.e. functionality of pdb2gmx is not implemented)
4. Generate files for each run separately, with a common name prefix (“deffnm”)
5. Lazy loading where possible
6. Safe default values according to the best practice
7. All responsibility lies with the user ]:-P