Re-add pre-minimisation to SOMD free-energy protocol configuration #59
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This PR closes #58. This wasn't essential, since the system is generally already minimised/equilibrated, but it seems to prevent some stability issues, presumably due to steric clashes due to fixed-precision loading from file, especially on GPU. A similar thing is seen for OpenMM, where it is often preferable to always run a short minimisation prior to any simulation.
Checklist:
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Suggested reviewers:
@chryswoods