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Currently the Sire-to-OpenMM code only sets default box vectors in the OpenMM system if the Sire system contains a periodic space. If not, then no box vectors are set. However, this doesn't mean that OpenMM doesn't use a periodic system, since it always uses a default 20A cubic box if no box vectors are set, e.g.:
In [1]: import sire as sr
In [2]: mols = sr.load_test_files("ala.crd", "ala.top")
In [3]: mols.remove_shared_property("space")
In [4]: d = mols[0].dynamics(cutoff="12 A")
In [5]: d.context().getState().getPeriodicBoxVectors()
Out[5]: Quantity(value=[Vec3(x=2.0, y=0.0, z=0.0), Vec3(x=0.0, y=2.0, z=0.0), Vec3(x=0.0, y=0.0, z=2.0)], unit=nanometer)This box might be completely inappropriate depending on the input system, e.g. if the molecule is too large, which would lead to self-interactions across the periodic boundary. When no periodic space is present, we should probably set sensible defaults based on the AABox of the system plus a buffer to account for the specified cut-off distance.
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