Fix issues #241, #242, and #243

[lohedges]

This PR...

closes #241
This removes shared properties when loading a perturbable system from file. This is needed to avoid issues when combining molecules together to form new systems. I've also added some extra logic into the GROMACS process code to check for a periodic system when updating the space property. For vacuum simulations we use a "fake" infinite box (as recommended by GROMACS) and I don't want to copy this property back if the original system contained an infinite cartesian space, which is now the default in Sire. Note that there was a typo in the existing code for readMolecules, which didn't cause any issues in practice since the property isn't used internally.

closes #242
This updates the error message to use the correct file names and removes the now redundant parmed import.

closes #243
This exposes the FreeEnergyMixin protocols, allowing GROMACS to run any existing protocol and intermediate lambda values, not just the end states. (This will be also be exposed for AMBER when ready.)

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

Suggested reviewers:

@chryswoods

[chryswoods]

Looks good. I think this is good motivation to (in future) add a "unshareProperties" or similar function to the sire Molecule so that it can automatically unshare all of its properties.