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Radius of Gyration needs wrap option #1760
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The I think what you want is |
yeah sorry, unwrap. Just forcing everything into the primary unit cell is definitely the wrong thing to do for the radius of gyration calculation. |
Should we change what |
P.S.: I created the new label:PBC – we have so many issues relating to periodic boundary conditions – a GSOC student digging into this would be great. |
I'd rather pbc=True was consistent in all methods (ie packs into unit cell
before calculation) but I agree that for Rgyr you actually want (the as yet
not implemented) unwrap=True kwarg instead.
…On Wed, 24 Jan 2018, 11:58 p.m. Oliver Beckstein, ***@***.***> wrote:
P.S.: I created the new label:PBC
<https://github.com/MDAnalysis/mdanalysis/labels/PBC> – we have so many
issues relating to periodic boundary conditions – a GSOC student digging
into this would be great.
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Then rather have unwrap=True and ditch useless pbc keyword. Rather be clear than opaque (or somesuch Python Zen).
… On Jan 24, 2018, at 5:28 PM, Richard Gowers ***@***.***> wrote:
I'd rather pbc=True was consistent in all methods (ie packs into unit cell
before calculation) but I agree that for Rgyr you actually want (the as yet
not implemented) unwrap=True kwarg instead.
--
Oliver Beckstein
orbeckst@gmail.com * orbeckst@gmx.net
|
I'm going to close this because it's a duplicate of #1185 |
I would like to keep this open as the |
Expected behaviour
Calculating correct radius of gyration when protein is split on the periodic boundary and we set
pbc=True
Actual behaviour
Neither with the pbc option set or without it do I get the correct radius of gyration. This is because to correctly handle the split of a protein on periodic boundaries we would need to recombine proteins that are split (unwrap them)
Example protein for which the correct value should be 2-4 nm.
Code to reproduce the behaviour
Currently version of MDAnalysis:
(run
python -c "import MDAnalysis as mda; print(mda.__version__)"
)The text was updated successfully, but these errors were encountered: