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orbeckst/polymer_rdf_COM.ipynb

Last active June 29, 2023 12:05
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Radial distribution function (RDF) calculation of the centers of mass of molecules with MDAnalysis.
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@orbeckst
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The first version that I posted was incorrect – the way that one replaces coordinates in the transformation is crucial: This is correct

self.com_atoms.positions = self.get_com()

but the following does not work

self.com_atoms.positions[:] = self.get_com()    # INCORRECT

(The reason is that .positions is a managed attribute that handles setting in a special way — you can't assume that you can just manipulate positions like a simple numpy array.)

@orbeckst
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Also note that the COM RDF looks a bit funny because it gets very close to r=0 even though self-distances had been excluded.

There's a possibility that this is a problem with unwrap=True. Please check carefully for your own system and let us know on the mailing list https://groups.google.com/group/mdnalysis-discussion

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