Fix amber fep mappings - protocol updates

[annamherz]

This PR is for further updates relating to running free energy simulations, copying settings from this branch.

• 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]

Changes:

• Updates to the FreeEnergy for data processing. This includes concat outside of the function, so that the preprocessing function can be used independently for other analysis outside of BSS. I also updated the truncate arguments for more clarity.
• All steps for reporting to 200 (from 250). This matches what is in the default protocol settings.
• 10 A cutoff for PME and 12 A for reaction field.
• Gromacs protocol softcore settings update for better default values, as well as some additional detail for the integrators/barostats.

Questions:

• In the process for Gromacs, only full perturbations are allowed. This is also the case previously for Amber in the free energy function. Does this need to be added to the Amber process?

Suggested reviewers:

@lohedges

[lohedges]

Thanks for this. The tweaks are now incorporated in to #366, so we can close this when you're happy.