Open kain88-de opened 6 years ago
The pbc
keyword will apply PBC by forcing everything into the primary unit cell.
I think what you want is unwrap
, to make the molecule whole and continuous, which is issue #1185 right?
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 pbc=True
does for radius_of_gyration()
? Do we have enough information to always correctly unwrap the selection?
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, notifications@github.com 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 notifications@github.com 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 pbc
keyword doesn't produce a correct result right now as one would expect. The bug should be open until it's removed.
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__)"
)