Fix issue #354 #355
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Fix issue #354 #355
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This PR closes #354 by rotating perturbable and non-perturbable molecules independently when rotating a simulation box as part of a reduction. Previously both sets of molecules were rotated at the same time, using the property map to specify the name of the coordinates (or velocity) property to use. This would raise an exception for the first molecule without this property, hence the actual perturbable ligand was never rotated.
develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]Tagging @mark-mackey-cresset so that you can test this.